U.S. patent number 7,846,455 [Application Number 10/722,000] was granted by the patent office on 2010-12-07 for attenuated chimeric respiratory syncytial virus.
This patent grant is currently assigned to N/A, The United States of America as represented by the Department of Health and Human Services. Invention is credited to Peter L. Collins, Brian R. Murphy, Stephen S. Whitehead.
United States Patent |
7,846,455 |
Collins , et al. |
December 7, 2010 |
Attenuated chimeric respiratory syncytial virus
Abstract
Chimeric respiratory syncytial virus (RSV) and vaccine
compositions thereof are produced by introducing one or more
heterologous gene(s) or gene segment(s) from one RSV subgroup or
strain into a recipient RSV backround of a different subgroup or
strain. The resulting chimeric RSV virus or subviral particle is
infectious and attenuated, preferably by introduction of selected
mutations specifying attenuated phenotypes into a chimeric genome
or antigenome to yield, for example, temperature sensitive (ts)
and/or cold adapted (ca) vaccine strains. Alternatively, chimeric
RSV and vaccine compositions thereof incorporate other mutations
specifying desired structural and/or phenotypic characteristics in
an infectious chimeric RSV. Such chimeric RSV incorporate desired
mutations specified by insertion, deletion, substitution or
rearrangement of one or more selected nucleotide sequence(s),
gene(s), or gene segment(s) in a chimeric RSV clone. This provides
a method for development of novel vaccines against diverse RSV
strains by using a common attenuated backbone as a vector to
express protective antigens of heterologous strains. The immune
system of an individual is stimulated to induce protection against
natural RSV infection, preferably in a multivalent manner to
achieve protection against multiple RSV strains and/or
subgroups.
Inventors: |
Collins; Peter L. (Rockville,
MD), Murphy; Brian R. (Bethesda, MD), Whitehead; Stephen
S. (Gaithersburg, MD) |
Assignee: |
The United States of America as
represented by the Department of Health and Human Services
(Washington, DC)
N/A (N/A)
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Family
ID: |
34557765 |
Appl.
No.: |
10/722,000 |
Filed: |
November 25, 2003 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20050100557 A1 |
May 12, 2005 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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09291894 |
Feb 10, 2004 |
6688367 |
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08892403 |
Jul 1, 2003 |
5993824 |
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60047634 |
May 23, 1997 |
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60046141 |
May 9, 1997 |
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60021773 |
Jul 15, 1996 |
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Current U.S.
Class: |
424/211.1;
435/239; 435/235.1; 435/236; 424/199.1; 424/204.1 |
Current CPC
Class: |
C12N
7/00 (20130101); C07K 14/005 (20130101); A61K
39/00 (20130101); C12N 2760/18522 (20130101); C12N
2760/18543 (20130101); A61K 2039/5254 (20130101); C12N
2760/18561 (20130101) |
Current International
Class: |
A61K
39/155 (20060101); C12N 7/04 (20060101); C12N
7/01 (20060101); C12N 7/00 (20060101); A61K
39/12 (20060101) |
References Cited
[Referenced By]
U.S. Patent Documents
Foreign Patent Documents
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Aug 1991 |
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EP |
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0 702 085 |
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Mar 1996 |
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EP |
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WO-93/21310 |
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Oct 1993 |
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WO |
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WO-97/06270 |
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Feb 1997 |
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WO |
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WO-97/12032 |
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Apr 1997 |
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WO |
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WO-97/20468 |
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Jun 1997 |
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WO |
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WO-98/02530 |
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Jan 1998 |
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WO |
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WO-98/43668 |
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Oct 1998 |
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WO |
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WO-99/15631 |
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Apr 1999 |
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WO |
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Primary Examiner: Lucas; Zachariah
Attorney, Agent or Firm: Woodcock Washburn LLP
Parent Case Text
RELATED APPLICATIONS
This The present application is a continuation of the prior
application Ser. No. 09/291,894, filed Apr. 13, 1999, and issued
Feb. 10, 2004 as U.S. Pat. No. 6,688,367, the benefit of the filing
date of which is hereby claimed under 35 USC 120, which in turn is
a continuation-in-part of U.S. patent application Ser. No.
08/892,403 filed Jul. 15, 1997 and issued Jul. 1, 2003 as U.S. Pat.
5,993,824, which in turn claims priority under 35 USC 119(e) of
U.S. Provisional Application Nos. 60/047,634 filed May 23, 1997 and
now abandoned, 60/046,141 filed May 9, 1997 and now abandoned, and
60/021,773 filed Jul. 15, 1996 and now abandoned, each of which is
incorporated herein by reference.
Claims
What is claimed is:
1. An infectious chimeric respiratory syncytial virus (RSV)
comprising a major nucleocapsid (N) protein, a nucleocapsid
phosphoprotein (P), a large polymerase protein (L), a RSV M2 ORF1
RNA polymerase elongation factor (M2(ORF1)), and a partial or
complete genome or antigenome of RSV A comprising genome segments
encoding antigenic determinants of RSV B F and G glycoproteins,
wherein the RSV A genome or antigenome contains the following
attenuating mutations: i) a mutation encoding V267I in the N gene;
ii) a mutation encoding C319Y in the L gene; iii) a mutation
encoding H1690Y in the L gene; iv) a mutation encoding Q831L in the
L gene; v) a mutation encoding D1183E in the L gene; vi) a point
mutation T to C at nucleotide 7605 of the gene start of the M2
gene; and wherein the RSV A genome or antigenome further contains
at least one of the following: a mutation encoding Y1321N in the L
gene; or a deletion of the SH open reading frame.
2. The chimeric RSV of claim 1, wherein the chimeric genome or
antigenome includes at least one attenuating mutation stabilized by
multiple nucleotide changes in a codon specifying the mutation.
3. The chimeric RSV of claim 1 further comprising a nucleotide
modification specifying a phenotypic change selected from a change
in growth characteristics, attenuation, temperature-sensitivity,
cold-adaptation, plaque size, host-range restriction, or a change
in immunogenicity.
4. The chimeric RSV of claim 3, wherein a SH, NS1, NS2, M2ORF2, or
G gene is modified.
5. The chimeric RSV of claim 4, wherein the SH, NS1, NS2, M2ORF2,
or G gene is deleted in whole or in part or expression of the gene
is ablated by introduction of one or more stop codons in an open
reading frame of the gene.
6. The chimeric RSV of claim 3, wherein the nucleotide modification
comprises an insertion, deletion, substitution, or rearrangement of
a translational start site within the chimeric genome or
antigenome.
7. The chimeric RSV of claim 1 which is a virus.
8. The chimeric RSV of claim 1 which is a subviral particle.
9. An immunogenic composition to elicit an immune response against
RSV comprising an immunologically sufficient amount of the chimeric
RSV of claim 1 in a physiologically acceptable carrier.
10. The immunogenic composition of claim 9, formulated in a dose of
10.sup.3 to 10.sup.6 PFU.
11. The immunogenic composition of claim 9, formulated for
administration to the upper respiratory tract by spray, droplet or
aerosol.
Description
BACKGROUND OF THE INVENTION
Human respiratory syncytial virus (RSV) outranks all other
microbial pathogens as a cause of pneumonia and bronchiolitis in
infants under one year of age. Virtually all children are infected
by two years of age, and reinfection occurs with appreciable
frequency in older children and young adults (Chanock et al., in
Viral Infections of Humans, 3rd ed., A. S. Evans, ed., Plenum
Press, N.Y. (1989). RSV is responsible for more than one in five
pediatric hospital admissions due to respiratory tract disease, and
causes an estimated 91,000 hospitalizations and 4,500 deaths yearly
in the United States alone. Although most healthy adults do not
have serious disease due to RSV infection, elderly patients and
immunocompromised individuals often suffer severe and possibly
life-threatening infections from this pathogen.
Despite decades of investigation to develop effective vaccine
agents against RSV, no safe and effective vaccine has yet been
achieved to prevent the severe morbidity and significant mortality
associated with RSV infection. Failure to develop successful
vaccines relates in part to the fact that small infants have
diminished serum and secretory antibody responses to RSV antigens.
Thus, these individuals suffer more severe infections from RSV,
whereas cumulative immunity appears to protect older children and
adults against more serious impacts of the virus. One antiviral
compound, ribavarin, has shown promise in the treatment of severely
infected infants, although there is no indication that it shortens
the duration of hospitalization or diminishes the infant's need for
supportive therapy.
The mechanisms of immunity in RSV infection have recently come into
focus. Secretory antibodies appear to be most important in
protecting the upper respiratory tract, whereas high levels of
serum antibodies are thought to have a major role in resistance to
RSV infection in the lower respiratory tract. Purified human
immunoglobulin containing a high titer of neutralizing antibodies
to RSV may prove useful in some instances of immunotherapeutic
approaches for serious lower respiratory tract disease in infants
and young children. Immune globulin preparations, however, suffer
from several disadvantages, such as the possibility of transmitting
blood-borne viruses and difficulty and expense in preparation and
storage.
RSV-specific cytotoxic T cells, another effector arm of induced
immunity, are also important in resolving an RSV infection.
However, while this latter effector can be augmented by prior
immunization to yield increased resistance to virus challenge, the
effect is short-lived. The F and G surface glycoproteins are the
two major protective antigens of RSV, and are the only two RSV
proteins which have been shown to induce RSV neutralizing
antibodies and long term resistance to challenge (Collins et al.,
Fields Virology, Fields et al. eds., 2:1313-1352. Lippincott-Raven,
Philadelphia. (1996); Connors et al., J. Virol. 65(3):1634-7
(1991)). The third RSV surface protein, SH, did not induce
RSV-neutralizing antibodies or significant resistance to RSV
challenge.
One obstacle to development of live RSV vaccines is the difficulty
in achieving an appropriate balance between attenuation and
immunogenicity. Genetic stability of attenuated viruses also can be
a problem. Vaccine development also is impeded by the relatively
poor growth of RSV in cell culture and the instability of the virus
particle. Another feature of RSV infection is that the immunity
which is induced is not fully protective against subsequent
infection. A number of factors probably contribute to this,
including the relative inefficiency of the immune system in
restricting virus infection on the luminal surface of the
respiratory tract, the short-lived nature of local mucosal
immunity, rapid and extensive virus replication, reduced immune
responses in the young due to immunological immaturity,
immunosuppression by transplacentally derived maternal serum
antibodies, and certain features of the virus such as a high degree
of glycosylation of the G protein. Also, as will be described
below, RSV exists as two antigenic subgroups A and B, and immunity
against one subgroup is of reduced effectiveness against the
other.
Although RSV can reinfect multiple times during life, reinfections
usually are reduced in severity due to protective immunity induced
by prior infection, and thus immunoprophylaxis is feasible. A
live-attenuated RSV vaccine would be administered intranasally to
initiate a mild immunizing infection. This has the advantage of
simplicity and safety compared to a parenteral route. It also
provides direct stimulation of local respiratory tract immunity,
which plays a major role in resistance to RSV. It also abrogates
the immunosuppressive effects of RSV-specific maternally-derived
serum antibodies, which typically are found in the very young.
Also, while the parenteral administration of RSV antigens can
sometimes be associated with immunopathologic complications (Murphy
et al., Vaccine 8(5):497-502 (1990)), this has never been observed
with a live virus.
Formalin-inactivated virus vaccine was tested against RSV in the
mid-1960s, but failed to protect against RSV infection or disease,
and in fact exacerbated symptoms during subsequent infection by the
virus. (Kim et al., Am. J. Epidemiol., 89:422-434 (1969), Chin et
al., Am J. Epidemiol., 89:449-463 (1969); Kapikian et al., Am. J.
Epidemiol., 89:405-421 (1969)).
More recently, vaccine development for RSV has focused on
attenuated RSV mutants. Friedewald et al., J. Amer. Med. Assoc.
204:690-694 (1968) reported a cold passaged mutant of RSV (cpRSV)
which appeared to be sufficiently attenuated to be a candidate
vaccine. This mutant exhibited a slight increased efficiency of
growth at 26.degree. C. compared to its wild-type (wt) parental
virus, but its replication was neither temperature sensitive nor
significantly cold-adapted. The cold-passaged mutant, however, was
attenuated for adults. Although satisfactorily attenuated and
immunogenic for infants and children who had been previously
infected with RSV (i.e., seropositive individuals), the cpRSV
mutant retained a low level virulence for the upper respiratory
tract of seronegative infants.
Similarly, Gharpure et al., J. Virol. 3:414-421 (1969) reported the
isolation of temperature sensitive RSV (tsRSV) mutants which also
were promising vaccine candidates. One mutant, ts-1, was evaluated
extensively in the laboratory and in volunteers. The mutant
produced asymptomatic infection in adult volunteers and conferred
resistance to challenge with wild-type virus 45 days after
immunization. Again, while seropositive infants and children
underwent asymptomatic infection, seronegative infants developed
signs of rhinitis and other mild symptoms. Furthermore, instability
of the ts phenotype was detected, although virus exhibiting a
partial or complete loss of temperature sensitivity represented a
small proportion of virus recoverable from vaccinees, and was not
associated with signs of disease other than mild rhinitis.
These and other studies revealed that certain cold-passaged and
temperature sensitive RSV strains were underattenuated and caused
mild symptoms of disease in some vaccinees, particularly
seronegative infants, while others were overattenuated and failed
to replicate sufficiently to elicit a protective immune response,
(Wright et al., Infect. Immun., 37:397-400 (1982)). Moreover,
genetic instability of candidate vaccine mutants has resulted in
loss of their temperature-sensitive phenotype, further hindering
development of effective RSV vaccines. See generally, Hodes et al.,
Proc. Soc. Exp. Biol. Med. 145:1158-1164 (1974), McIntosh et al.,
Pediatr. Res. 8:689-696 (1974), and Belshe et al., J. Med. Virol.,
3:101-110 (1978).
Abandoning the approach of creating suitably attenuated RSV strains
through undefined biological methods such as cold-passaging,
investigators tested subunit vaccine candidates using purified RSV
envelope glycoproteins. The glycoproteins induced resistance to RS
virus infection in the lungs of cotton rats, Walsh et al., J.
Infect. Dis. 155:1198-1204 (1987), but the antibodies had very weak
neutralizing activity and immunization of rodents with purified
subunit vaccine led to disease potentiation (Murphy et al., Vaccine
8:497-502 (1990)).
Vaccinia virus recombinant-based vaccines which express the F or G
envelope glycoprotein have also been explored. These recombinants
express RSV glycoproteins which are indistinguishable from the
authentic viral counterpart, and rodents infected intradermally
with vaccinia-RSV F and G recombinants developed high levels of
specific antibodies that neutralized viral infectivity. Indeed,
infection of cotton rats with vaccinia-F recombinants stimulated
almost complete resistance to replication of RSV in the lower
respiratory tract and significant resistance in the upper tract.
Olmsted et al., Proc. Natl. Acad. Sci. USA 83:7462-7466 (1986).
However, immunization of chimpanzees with vaccinia-F and -G
recombinant provided almost no protection against RSV challenge in
the upper respiratory tract (Collins et al., Vaccine 8:164-168
(1990)) and inconsistent protection in the lower respiratory tract
(Crowe et al., Vaccine 11:1395-1404 (1993).
The unfulfilled promises of attenuated RSV strains, subunit
vaccines, and other strategies for RSV vaccine development
underscores a need for new methods to develop novel RSV vaccines,
particularly methods for manipulating recombinant RSV to
incorporate genetic changes to yield new phenotypic properties in
viable, attenuated RSV recombinants. However, manipulation of the
genomic RNA of RSV and other negative-sense RNA viruses has
heretofore proven difficult. Major obstacles in this regard include
non-infectivity of naked genomic RNA of these viruses, poor viral
growth in tissue culture, lengthy replication cycles, virion
instability, a complex genome, and a refractory organization of
gene products.
Recombinant DNA technology has made it possible to recover
infectious negative-stranded RNA viruses from cDNA, to genetically
manipulate viral clones to construct novel vaccine candidates, and
to rapidly evaluate their level of attenuation and phenotypic
stability (for reviews, see Conzelmann, J. Gen. Virol. 77:381-89
(1996); Palese et al., Proc. Natl. Acad. Sci. U.S.A. 93:11354-58,
(1996)). In this context, recombinant rescue has been reported for
infectious respiratory syncytial virus (RSV), parainfluenza virus
(PIV), rabies virus (RaV), vesicular stomatitis virus (VSV),
measles virus (MeV), and Sendai virus (SeV) from cDNA-encoded
antigenomic RNA in the presence of essential viral proteins (see,
e.g., Garcin et al., EMBO J. 14:6087-6094 (1995); Lawson et al.,
Proc. Natl. Acad. Sci. U.S.A. 92:4477-81 (1995); Radecke et al.,
EMBO J. 14:5773-5784 (1995); Schnell et al., EMBO J. 13:4195-203
(1994); Whelan et al., Proc. Natl. Acad. Sci. U.S.A. 92:8388-92
(1995); Hoffman et al., J. Virol. 71:4272-4277 (1997); Kato et al.,
Genes to Cells 1:569-579 (1996), Roberts et al., Virology 247(1),
1-6 (1998); Baron et al., J. Virol. 71:1265-1271 (1997);
International Publication No. WO 97/06270; Collins et al., Proc.
Natl. Acad. Sci. USA 92:11563-11567 (1995); Durbin et al., Virology
235:323-332 (1997); U.S. patent application Ser. No. 08/892,403,
filed Jul. 15, 1997 (corresponding to published International
Application No. WO 98/02530 and priority U.S. Provisional
Application Nos. 60/047,634, filed May 23, 1997, 60/046,141, filed
May 9, 1997, and 60/021,773, filed Jul. 15, 1996); Juhasz et al.,
J. Virol. 71(8):5814-5819 (1997); He et al. Virology 237:249-260
(1997); Baron et al. J. Virol. 71:1265-1271 (1997); Whitehead et
al., Virology 247(2):232-9 (1998a); Whitehead et al., J. Virol.
72(5):4467-4471 (1998b); Jin et al. Virology 251:206-214 (1998);
Bucholz et al. J. Virol. 73:251-259 (1999); and Whitehead et al.,
J. Virol. 73:(4)3438-3442 (1999), each incorporated herein by
reference).
Among the remaining challenges to RSV vaccine development is the
difficulty of achieving vaccine candidates that are effective
against a broad range of existing and emergent strains and
subgroups of RSV. In particular, it will be useful to provide a RSV
subgroup B-specific vaccine virus, as well as multivalent vaccines
to provide protection against both RSV A and RSV B subgroups. In
this context, recent research has focused on development of
chimeric viruses to carry antigenic determinants between viral
strains. For example, the HN and F glycoproteins of human
parainfluenza virus type 3 (PIV3) have been replaced by those of
human parainfluenza virus type 1 (HPIV1), and the resulting
chimeric virus grew in cell culture and in experimental animals
with an efficiency similar to its wild-type parents (Tao et al., J.
Virol. 72(4):2955-61 (1998), incorporated herein by reference. Also
reported is a chimeric measles virus where the H and F
glycoproteins were replaced with the G glycoprotein of vesicular
stomatitis virus, which was inserted with or without replacement of
the cytoplasmic and transmembrane region of G with that of measles
virus F (Spielhofer et al., J. Virol. 72(3):2150-9 (1998)). This
yielded a chimeric virus that was reportedly 50-fold reduced in
growth. In a third example, Jin et al., Virology 251(1):206-14
(1998) report a subgroup A virus which expresses the G protein of a
subgroup B RSV as an additional gene (Jin et al., Virology
251(1):206-14 (1998)). However, since the F protein also exhibits
significant subgroup-specificity, it would be preferable to express
both subgroup B glycoproteins in a subgroup B-specific vaccine. In
addition, production of a chimeric A-B virus will not produce a
viable vaccine candidate without further modifications to achieve
proper attenuation and virulence.
Accordingly, an urgent need remains in the art for tools and
methods to engineer safe and effective vaccines to alleviate the
serious health problems attributable to RSV, particularly that will
be effective against multiple existing and emergent strains and
subgroups of RSV. Quite surprisingly, the present invention
satisfies these and other related needs.
SUMMARY OF THE INVENTION
The present invention provides chimeric, recombinant respiratory
syncytial virus (RSV) that are infectious and elicit a propylactic
or therapeutic immune response in humans or other mammals. In
related aspects, the invention provides novel methods and
compositions for designing and producing attenuated, chimeric RSV
suitable for vaccine use. Included within these aspects of the
invention are novel, isolated polynucleotide molecules and vectors
incorporating such molecules that comprise a chimeric RSV genome or
antigenome including a partial or complete RSV genome or antigenome
of one RSV strain or subgroup virus combined with one or more
heterologous gene(s) or gene segment(s) of a different RSV strain
or subgroup virus. Also provided within the invention are methods
and compositions incorporating chimeric, recombinant RSV for
prophylaxis and treatment of RSV infection.
Chimeric RSV of the invention are recombinantly engineered to
incorporate nucleotide sequences from more than one RSV strain or
subgroup to produce an infectious, chimeric virus or subviral
particle. In this manner, candidate vaccine viruses are
recombinantly engineered to elicit an immune response against RSV
in a mammalian host susceptible to RSV infection, including humans
and non-human primates. Chimeric RSV according to the invention may
elicit an immune response to a specific RSV subgroup or strain, or
a polyspecific response against multiple RSV subgroups or
strains.
Exemplary chimeric RSV of the invention incorporate a chimeric RSV
genome or antigenome, as well as a major nucleocapsid (N) protein,
a nucleocapsid phosphoprotein (P), a large polymerase protein (L),
and a RNA polymerase elongation factor. Additional RSV proteins may
be included in various combinations to provide a range of
infectious subviral particles as well as complete viral
particles.
Chimeric RSV of the invention include a partial or complete RSV
genome or antigenome from one RSV strain or subgroup virus combined
with one or more heterologous gene(s) or gene segment(s) of a
different RSV strain or subgroup virus to form the chimeric RSV
genome or antigenome. In preferred aspects of the invention,
chimeric RSV incorporate a partial or complete human RSV genome or
antigenome of one RSV subgroup or strain combined with one or more
heterologous gene(s) or gene segment(s) from a different human RSV
subgroup or strain. For example, a chimeric RSV may incorporate a
chimeric genome or antigenome comprised of a partial or complete
human RSV A subgroup genome or antigenome combined with one or more
heterologous gene(s) or gene segment(s) from a human RSV B subgroup
virus.
Heterologous genes or gene segments from one RSV strain or subgroup
represent "donor" genes or polynucleotides that are combined with,
or substituted within, a "recipient" genome or antigenome. The
recipient genome or antigenome typically acts as a "backbone" or
vector to import heterologous genes or gene segments to yield a
chimeric RSV exhibiting novel phenotypic characteristics. For
example, addition or substitution of heterologous genes or gene
segments within a selected recipient RSV strain may result in
attenuation, growth changes, altered immunogenicity, or other
desired phenotypic changes as compared with a corresponding
phenotype(s) of the unmodified recipient and/or donor. Genes and
gene segments that may be selected for use as heterologous inserts
or additions within the invention include genes or gene segments
encoding a NS1, NS2, N, P, M, SH, M2(ORF1), M2(ORF2), L, F or G
protein or portion thereof.
In preferred embodiments of the invention, chimeric RSV
incorporates one or more heterologous gene(s) that encode an RSV F,
G or SH glycoprotein. Alternatively, the chimeric RSV may
incorporate a gene segment encoding a cytoplasmic domain,
transmembrane domain, ectodomain or immunogenic epitope of a RSV F,
G or SH glycoprotein. These immunogenic proteins, domains and
epitopes are particularly useful within chimeric RSV because they
can generate novel immune responses in an immunized host.
For example, addition or substitution of one or more immunogenic
gene(s) or gene segment(s) from one donor RSV subgroup or strain
within a recipient genome or antigenome of a different RSV subgroup
or strain can generate an immune response directed against the
donor subgroup or strain or against both the donor and recipient
subgroup or strain. In one exemplary embodiment, one or more human
RSV subgroup B glycoprotein genes F, G and SH or a cytoplasmic
domain, transmembrane domain, ectodomain or immunogenic epitope
thereof, is added to, or substituted within, an RSV A genome or
antigenome.
In additional aspects of the invention, attenuated, chimeric RSV
are produced in which the chimeric genome or antigenome is further
modified by introducing one or more attenuating point mutations
specifying an attenuating phenotype. These point mutations may be
generated de novo and tested for attenuating effects according to a
rational design mutagenesis strategy. Alternatively, the
attenuating point mutations are identified in biologically derived
mutant RSV and thereafter incorporated into a chimeric RSV of the
invention.
Preferably, chimeric RSV of the invention are attenuated by
incorporation of at least one, and more preferably two or more,
attenuating point mutations identified from a panel of known,
biologically derived mutant RSV strains. Preferred mutant RSV
strains described herein are cold passaged (cp) and/or temperature
sensitive (ts) mutants, for example the mutants designated "cpts
RSV 248 (ATCC VR 2450), cpts RSV 248/404 (ATCC VR 2454), cpts RSV
248/955 (ATCC VR 2453), cpts RSV 530 (ATCC VR 2452), cpts RSV
530/1009 (ATCC VR 2451), cpts RSV 530/1030 (ATCC VR 2455), RSV B-1
cp52/2B5 (ATCC VR 2542), and RSV B-1 cp-23 (ATCC VR 2579)" (each
deposited under the terms of the Budapest Treaty with the American
Type Culture Collection (ATCC) of 10801 University Boulevard,
Manassas, Va. 20110-2209, U.S.A., and granted the above identified
accession numbers). From this exemplary panel of biologically
derived mutants, a large "menu" of attenuating mutations are
provided which can each be combined with any other mutation(s)
within the panel for calibrating the level of attenuation in the
recombinant, chimeric RSV for vaccine use. Additional mutations may
be derived from RSV having non-ts and non-cp attenuating mutations
as identified, e.g., in small plaque (sp), cold-adapted (ca) or
host-range restricted (hr) mutant strains.
In yet additional aspects of the invention, chimeric RSV, with or
without attenuating point mutations, are mutated by a non-point
nucleotide modification to produce desired phenotypic, structural,
or functional changes. Typically, the selected nucleotide
modification will specify a phenotypic change, for example a change
in growth characteristics, attenuation, temperature-sensitivity,
cold-adaptation, plaque size, host range restriction, or
immunogenicity. Structural or functional changes include
introduction or ablation of restriction sites into RSV encoding
cDNAs for ease of manipulation and identification.
In preferred embodiments, an SH, NS1, NS2 or G gene is modified in
the chimeric RSV, e.g., by deletion of the gene or ablation of its
expression. Alternatively, the nucleotide modification can include
a deletion, insertion, addition or rearrangement of a cis-acting
regulatory sequence for a selected RSV gene.
In one example, a cis-acting regulatory sequence of one RSV gene is
changed to correspond to a heterologous regulatory sequence, which
may be a counterpart cis-acting regulatory sequence of the same
gene in a different RSV or a cis-acting regulatory sequence of a
different RSV gene. For example, a gene end signal may be modified
by conversion or substitution to a gene end signal of a different
gene in the same RSV strain.
In a separate embodiment, the nucleotide modification may comprise
an insertion, deletion, substitution, or rearrangement of a
translational start site within the chimeric genome or antigenome,
e.g., to ablate an alternative translational start site for a
selected form of a protein. In one example, the translational start
site for a secreted form of the RSV G protein is ablated to modify
expression of this form of the G protein and thereby produce
desired in vivo effects.
Yet additional modifications may be made to the chimeric RSV genome
or antigenome according to the invention, including modifications
that introduce into the chimeric genome or antigenome a non-RSV
molecule such as cytokine, a T-helper epitope, a restriction site
marker, or a protein of a microbial pathogen capable of eliciting a
protective immune response against the pathogen in a mammalian
host. In one such embodiment, chimeric RSV are constructed that
incorporate a gene or gene segment from a parainfluenza virus
(PIV), for example a PIV HN or F glycoprotein or an immunogenic
domain or epitope thereof.
Chimeric RSV designed and selected for vaccine use often have at
least two and sometimes three or more attenuating mutations to
achieve a satisfactory level of attenuation for broad clinical use.
In one embodiment, at least one attenuating mutation occurs in the
RSV polymerase gene (either in the donor or recipient gene) and
involves one or more nucleotide substitution(s) specifying an amino
acid change in the polymerase protein specifying an attenuation
phenotype which may or may not involve a temperature-sensitive (ts)
phenotype. Exemplary chimeric RSV in this context incorporate one
or more nucleotide substitutions in the large polymerase gene L
resulting in an amino acid change at amino acid Phe.sub.521,
Gln.sub.831, Met.sub.1169, or Tyr.sub.1321, as exemplified by the
changes, Leu for Phe.sub.521, Leu for Gln.sub.831, Val for
Met.sub.1169, and Asn for Tyr.sub.1321. Other alternative amino
acid assignments at this position can of course be made to yield a
similar effect as the identified, mutant substitution. In this
context, it is preferable to modify the chimeric genome or
antigenome to encode an alteration at the subject site of mutation
that corresponds conservatively to the alteration identified in the
mutant virus. For example, if an amino acid substitution marks a
site of mutation in the mutant virus compared to the corresponding
wild-type sequence, then a similar substitution should be
engineered at the corresponding residue(s) in the recombinant
virus. Preferably the substitution will involve an identical or
conservative amino acid to the substitute residue present in the
mutant viral protein. However, it is also possible to alter the
native amino acid residue at the site of mutation
non-conservatively with respect to the substitute residue in the
mutant protein (e.g., by using any other amino acid to disrupt or
impair the identity and functio of the wild-type residue). In the
case of mutations marked by deletions or insertions, these can be
introduced as corresponding deletions or insertions into the
recombinant virus, however the particular size and amino acid
sequence of the deleted or inserted protein fragment can vary.
Chimeric RSV of the invention may incorporate a ts mutation in any
additional RSV gene besides L, e.g., in the M2 gene.
Preferably, two or more nucleotide changes are incorporated in a
codon specifying an attenuating mutation, e.g., in a codon
specifying a ts mutation, thereby decreasing the likelihood of
reversion from an attenuated phenotype.
Attenuating mutations may be selected in coding portions of a donor
or recipient RSV gene or in non-coding regions such as a
cis-regulatory sequence. Exemplary non-coding mutations include
single or multiple base changes in a gene start sequence, as
exemplified by a single or multiple base substitution in the M2
gene start sequence at nucleotide 7605 (nucleotide 7606 in
recombinant sequence).
In another aspect of the invention, compositions (e.g., isolated
polynucleotides and vectors incorporating an RSV-encoding cDNA) and
methods are provided for producing an isolated infectious chimeric
RSV. Using these compositions and methods, infectious chimeric RSV
are generated from a chimeric RSV genome or antigenome, a
nucleocapsid (N) protein, a nucleocapsid phosphoprotein (P), a
large (L) polymerase protein, and an RNA polymerase elongation
factor. In related aspects of the invention, compositions and
methods are provided for introducing the aforementioned structural
and phenotypic changes into a recombinant chimeric RSV to yield
infectious, attenuated vaccine viruses.
In one embodiment, an expression vector is provided which comprises
an isolated polynucleotide molecule encoding a chimeric RSV genome
or antigenome. Also provided is the same or different expression
vector comprising one or more isolated polynucleotide molecules
encoding N, P, L and RNA polymerase elongation factor proteins. The
vector(s) is/are preferably expressed or coexpressed in a cell or
cell-free lysate, thereby producing an infectious chimeric RSV
particle or subviral particle.
The RSV genome or antigenome and the N, P, L and RNA polymerase
elongation factor (preferably the product of the M2(ORF1) of RSV)
proteins can be coexpressed by the same or different expression
vectors. In some instances the N, P, L and RNA polymerase
elongation factor proteins are each encoded on different expression
vectors. The polynucleotide molecule encoding the chimeric RSV
genome or antigenome can be a chimera of different human RSV
subgroups or strains, for example a polynucleotide containing
sequences from a subgroup A RSV operably joined with sequences from
a subgroup B RSV. Alternatively, the chimeric genome or antigenome
can be a chimera of human and non-human (e.g., bovine or murine)
RSV sequences. In yet another alternative aspect of the invention,
the chimeric genome or antigenome can be a chimera of RSV and
non-RSV sequences, for example a polynucleotide containing
sequences from a human RSV operably joined with PIV sequences. The
chimeric genome or antigenome can be further modified by insertion,
rearrangement, deletion or substitution of one or more nucleotides,
including point mutations, site-specific nucleotide changes, and
changes involving entire genes or gene segments introduced within a
heterologous donor gene or gene segment or the recipient,
background genome or antigenome. These alterations typically
specify one or more phenotypic change(s) in the resulting
recombinant RSV, such as a phenotypic change that results in
attenuation, temperature-sensitivity, cold-adaptation, small plaque
size, host range restriction, alteration in gene expression, or a
change in an immunogenic epitope.
The above methods and compositions for producing chimeric RSV yield
infectious viral or subviral particles, or derivatives thereof. An
infectious virus is comparable to the authentic RSV virus particle
and is infectious as is. It can directly infect fresh cells. An
infectious subviral particle typically is a subcomponent of the
virus particle which can initiate an infection under appropriate
conditions. For example, a nucleocapsid containing the genomic or
antigenomic RNA and the N, P, L and M2(ORF1) proteins is an example
of a subviral particle which can initiate an infection if
introduced into the cytoplasm of cells. Subviral particles provided
within the invention include, inter alia, viral particles which
lack one or more protein(s), protein segment(s), or other viral
component(s) not essential for infectivity.
Infectious chimeric RSV according to the invention can incorporate
heterologous, coding or non-coding nucleotide sequences from any
RSV or RSV-like virus, e.g., human, bovine, murine (pneumonia virus
of mice), or avian (turkey rhinotracheitis virus) RSV, or from
another enveloped virus, e.g., parainfluenza virus (PIV). In
exemplary aspects, the recombinant RSV comprises a chimera of a
human RSV genomic or antigenomic sequence recombinantly joined with
one or more heterologous RSV sequence(s). Exemplary heterologous
sequences include RSV sequences from one human RSV strain combined
with sequences from a different human RSV strain. For example,
chimeric RSV of the invention may incorporate sequences from two or
more wild-type or mutant RSV strains, for example mutant strains
selected from cpts RSV 248, cpts 248/404, cpts 248/955, cpts RSV
530, cpts 530/1009, or cpts 530/1030). Alternatively, chimeric RSV
may incorporate sequences from two or more, wild-type or mutant RSV
subgroups, for example a combination of RSV subgroup A and subgroup
B sequences. In yet additional aspects, one or more human RSV
coding or non-coding polynucleotides are substituted with a
counterpart sequence from bovine or murine RSV, alone or in
combination with one or more selected attenuating point mutations,
e.g., cp and/or ts mutations, to yield novel attenuated vaccine
strains. In one embodiment, a chimeric bovine-human RSV
incorporates a substitution of the human RSV NP gene or gene
segment with a counterpart bovine NP gene or gene segment, which
chimera can optionally be constructed to incorporate a SH gene
deletion, one or more cp or ts point mutations, or various
combinations of these and other mutations disclosed herein.
In one embodiment of the invention, isolated polynucleotides,
expression vectors, and methods for producing chimeric RSV are
provided wherein the genome or antigenome is recombinantly altered
compared to either the donor or recipient sequence. In particular,
mutations are incorporated within a chimeric RSV genome or
antigenome based on their ability to alter the structure and/or
function of a chimeric RSV clone, e.g., by altering the structure,
expression and or function of a selected protein encoded or a
cis-acting RNA sequence thereby yielding a desired phenotypic
change. Desired phenotypic changes include, e.g., changes in viral
growth in culture, temperature sensitivity, plaque size,
attenuation, and immunogenicity.
In one aspect of the invention, isolated polynucleotides and
expression vectors are provided which comprise a chimeric RSV
genome or antigenome having at least one attenuating point mutation
adopted from a biologically derived mutant RSV. In one such
embodiment, at least one point mutation is present in the
polymerase gene L involving a nucleotide substitution that
specifies a ts phenotype., Exemplary RSV clones and vectors
incorporate a nucleotide substitution that results in an amino acid
change in the polymerase gene at Phe.sub.521, Gln.sub.831,
Met.sub.1169, or Tyr.sub.1321. Preferably, two or three mutations
are incorporated in a codon specifying the attenuating mutation in
order to increase the level of genetic stability. Other exemplary
RSVs incorporate at least two attenuating ts mutations.
Mutations incorporated within chimeric cDNAs, vectors and viral
particles of the invention can be introduced individually or in
combination into a full-length RSV cDNA and the phenotypes of
rescued virus containing the introduced mutations can be readily
determined. In exemplary embodiments, amino acid changes displayed
by attenuated, biologically-derived viruses versus a wild-type RSV,
for example changes exhibited by cpRSV or tsRSV, are incorporated
in combination within recombinant RSV to yield a desired level of
attenuation.
The present invention also provides chimeric RSV clones, vectors
and particles incorporating multiple, phenotype-specific mutations
introduced in selected combinations into the chimeric genome or
antigenome to produce an attenuated, infectious virus or subviral
particle. This process, coupled with routine phenotypic evaluation,
provides chimeric RSV having such desired characteristics as
attenuation, temperature sensitivity, altered immunogenicity,
cold-adaptation, small plaque size, host range restriction, etc.
Mutations thus identified are compiled into a "menu" and introduced
in various combinations to calibrate a vaccine virus to a selected
level of attenuation, immunogenicity and stability.
In preferred embodiments, the invention provides for
supplementation of one or more mutations adopted from biologically
derived RSV, e.g., cp and ts mutations, with additional types of
mutations involving the same or different genes. Target genes for
mutation in this context include the attachment (G) protein, fusion
(F) protein, small hydrophobic (SH), RNA binding protein (N),
phosphoprotein (P), the large polymerase protein (L), the
transcription elongation factor (M2), M2 ORF2, the matrix (M)
protein, and two nonstructural proteins, NS1 and NS2. Each of these
proteins can be selectively deleted, substituted or rearranged, in
whole or in part, alone or in combination with other desired
modifications, to achieve novel chimeric RSV recombinants.
In one aspect, the SH gene is deleted in the donor or recipient
context to yield a chimeric RSV having novel phenotypic
characteristics, including enhanced growth in vitro and/or
attenuation in vivo. In a related aspect, this gene deletion, or
another selected, non-essential gene or gene segment deletion, such
as a NS1 or NS2 gene deletion is combined in a chimeric RSV with
one or more separate mutations specifying an attenuated phenotype,
e.g., a point mutation adopted directly (or in modified form, e.g.,
by introducing multiple nucleotide changes in a codon specifying
the mutation) from a biologically derived attenuated RSV
mutant.
For example, the SH gene or NS2 gene may be deleted in combination
with one or more cp and/or ts mutations adopted from cpts248/404,
cpts530/1009, cpts530/1030, or another selected mutant RSV strain,
to yield a chimeric RSV having increased yield of virus, enhanced
attenuation, and genetic resistance to reversion from an attenuated
phenotype, due to the combined effects of the different
mutations.
In addition, a variety of other genetic alterations can be produced
in a chimeric RSV genome or antigenome, alone or together with one
or more attenuating point mutations adopted from a biologically
derived mutant RSV. For example, genes or gene segments from
non-RSV sources may be inserted in whole or in part. Alternatively,
the order of genes can be changed, gene overlap removed, or a RSV
genome promoter replaced with its antigenome counterpart. Different
or additional modifications in the chimeric genome or antigenome
can be made to facilitate manipulations, such as the insertion of
unique restriction sites in various intergenic regions (e.g., a
unique Stul site between the G and F genes) or elsewhere.
Nontranslated gene sequences can be removed to increase capacity
for inserting foreign sequences.
Alternatively, polynucleotide molecules or vectors encoding the
chimeric RSV genome or antigenome can be modified to encode non-RSV
sequences, e.g., a cytokine, a T-helper epitope, a restriction site
marker, or a protein of a microbial pathogen (e.g., virus,
bacterium or fungus) capable of eliciting a protective immune
response in an intended host.
In other embodiments the invention provides a cell or cell-free
lysate containing an expression vector which comprises an isolated
polynucleotide molecule encoding a chimeric RSV genome or
antigenome as described above, and an expression vector (the same
or different vector) which comprises one or more isolated
polynucleotide molecules encoding the N, P, L and RNA polymerase
elongation factor proteins of RSV. Upon expression the genome or
antigenome and N, P, L, and RNA polymerase elongation factor
proteins combine to produce an infectious RSV viral or subviral
particle.
Attenuated chimeric RSV of the invention is capable of eliciting a
protective immune response in an infected human host, yet is
sufficiently attenuated so as to not cause unacceptable symptoms of
severe respiratory disease in the immunized host. The attenuated
chimeric virus or subviral particle may be present in a cell
culture supernatant, isolated from the culture, or partially or
completely purified. The virus may also be lyophilized, and can be
combined with a variety of other components for storage or delivery
to a host, as desired.
The invention further provides novel vaccines comprising a
physiologically acceptable carrier and/or adjuvant and an isolated
attenuated chimeric RSV as described above. In one embodiment, the
vaccine is comprised of chimeric RSV having at least one, and
preferably two or more attenuating mutations or other nucleotide
modifications as described above. The vaccine can be formulated in
a dose of 10.sup.3 to 10.sup.6 PFU of attenuated virus. The vaccine
may comprise attenuated chimeric virus that elicits an immune
response against a single RSV strain or antigenic subgroup, e.g. A
or B, or against multiple RSV strains or subgroups. In this regard,
chimeric RSV of the invention can individually elicit a
monospecific immune response or a polyspecific immune response
against multiple RSV strains or subgroups. Chimeric RSV can be
combined in vaccine formulations with other chimeric RSV or
non-chimeric RSV having different immunogenic characteristics for
more effective protection against one or multiple RSV strains or
subgroups.
In related aspects, the invention provides a method for stimulating
the immune system of an individual to elicit an immune response
against one or more strains or subgroups of RSV in a mammalian
subject. The method comprises administering a formulation of an
immunologically sufficient amount of an attenuated, chimeric RSV as
described above in a physiologically acceptable carrier and/or
adjuvant. In one embodiment, the immunogenic composition is a
vaccine comprised of chimeric RSV having at least one, and
preferably two or more attenuating mutations or other nucleotide
modifications as described above. The vaccine can be formulated in
a dose of 10.sup.3 to 10.sup.6 PFU of attenuated virus. The vaccine
may comprise attenuated chimeric virus that elicits an immune
response against a single RSV strain or antigenic subgroup, e.g. A
or B, or against multiple RSV strains or subgroups. In this
context, the chimeric RSV can elicit a monospecific immune response
or a polyspecific immune response against multiple RSV strains or
subgroups. Alternatively, chimeric RSV having different immunogenic
characteristics can be combined in a vaccine mixture or
administered separately in a coordinated treatment protocol to
elicit more effective protection against one RSV strain, or against
multiple RSV strains or subgroups.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a graph demonstrating the substantially complete
correlation between the replication of a series of subgroup A
respiratory syncytial viruses in the lungs of mice with their
replication in the chimpanzee.
FIGS. 2 and 3 show the construction of cDNA encoding RSV antigenome
RNA, where FIG. 2 shows the structures of the cDNA and the encoded
antigenome RNA (not to scale). For the purposes of the present
Figures, and in all subsequent Examples hereinbelow, the specific
cDNAs and viruses used were of strain A2 of subgroup A RSV. The
diagram of the antigenome includes the following features: the
5'-terminal nonviral G triplet contributed by the T7 promoter, the
four sequence markers at positions 1099 (which adds one nt to the
length), 1139, 5611, and 7559 (numbering referring to the first
base of the new restriction site), the ribozyme and tandem T7
terminators, and the single nonviral 3'-phosphorylated U residue
contributed to the 3' end by ribozyme cleavage (the site of
cleavage is indicated with an arrow). Note that the nonviral 5'-GGG
and 3'-U residues are not included in length values given here and
thereafter for the antigenome. However, the nucleotide insertion at
position 1099 is included, and thus the numbering for cDNA-derived
antigenome is one nucleotide greater downstream of this position
than for biologically derived antigenome. The 5' to 3'
positive-sense sequence of D46 (the genome itself being
negative-sense) is depicted in SEQ ID NO: 1, where the nucleotide
at position four can be either C or G. Also note that the sequence
positions assigned to restriction sites in this Figure and
throughout are intended as a descriptive guide and do not alone
define all of the nucleotides involved. The length values assigned
to restriction fragments here and throughout also are descriptive,
since length assignments may vary based on such factors as sticky
ends left following digestion. Cloned cDNA segments representing in
aggregate the complete antigenome are also shown. The box
illustrates the removal of the BamHI site from the plasmid vector,
a modification that facilitated assembly: the naturally occurring
BamHI-SalI fragment (the BamHI site is shown in the top line in
positive sense, underlined) was replaced with a PCR-generated
BglII-SalI fragment (the BglII site is shown in the bottom line,
underlined; its 4-nt sticky end, shown in italics, is compatible
with that of BamHI). This resulted in a single nt change (middle
line, underlined) which was silent at the amino acid level. FIG. 3
shows the sequence markers contained in the cDNA-encoded antigenome
RNA, where sequences are positive sense and numbered relative to
the first nt of the leader region complement as 1; identities
between strains A2 and 18537, representing RSV subgroups A and B,
respectively, are indicated with dots; sequences representing
restriction sites in the cDNA are underlined; gene-start (GS) and
gene-end (GE) transcription signals are boxed; the initiation codon
of the N translational open reading frame at position 1141 is
italicized, and the restriction sites are shown underneath each
sequence. In the top sequence (SEQ ID NO. 22), a single C residue
was inserted at position 1099 to create an AflII site in the NS2-N
intergenic region, and the AG at positions 1139 and 1140
immediately upstream of the N translational open reading frame were
replaced with CC to create a new NcoI site. In the middle sequence
(SEQ ID NO. 23), substitution of G and U at positions 5612 and
5616, respectively, created a new Stul site in the G-F intergenic
region. In the bottom sequence (SEQ ID NO. 24), a C replacement at
position 7560 created a new SphI site in the F-M2intergenic
region.
FIG. 4 illustrates structures of cDNAs (approximately to scale)
involved in the insertion of mutations, assembly of complete
antigenome constructs, and recovery of recombinant virus. Four
types of mutations were inserted into the pUC118- or pUC119-borne
cDNA subclones shown in the bottom row, namely six silent
restriction sites in the L gene (underlined over the D53 diagram on
the top), two HEK changes in the F gene (H), five cp changes (cp),
and the mutations specific to the various biological mutagenesis
steps: 248, 404, 530, 1009, and 1030 (as indicated). The
mutagenized subclones were inserted into the D50 (representing the
RSV antigenome from the leader to the beginning of the M2-L overlap
with the T7 promoter immediately upstream of the leader) or D39
(representing the RSV antigenome from the M2-L overlap to the
trailer with the ribozyme and T7 terminators immediately downstream
of the trailer) intermediate plasmids shown in the middle row. The
appropriate D50 and D39 were assembled into full-length D53
antigenome cDNA as shown on the top row (RTT indicates the location
of the hammer-head ribozyme followed by two T7 transcription
terminators).
FIG. 5 provides maps of six mutant antigenome cDNAs which were used
to recover recombinant RSV. The ts phenotypes of the recombinants
are summarized on the right of the figure.
FIG. 6 shows construction of D46/1024CAT cDNA encoding an RSV
antigenome containing the CAT ORF flanked by RSV transcription
signals (not to scale, RSV-specific segments are shown as filled
boxes and CAT sequence as an open box). The source of the CAT gene
transcription cassette was RSV-CAT minigenome cDNA 6196(diagram at
top). The RSV-CAT minigenome contains the leader region, GS and GE
signals, noncoding (NC) RSV gene sequences, and the CAT ORF, with
XmaI restriction endonuclease sites preceding the GS signal and
following the GE signal (5' and 3' sequences are shown, SEQ ID NOs.
25 and 26, respectively). The nucleotide lengths of these elements
are indicated, and the sequences (positive-sense) surrounding the
XmaI sites are shown above the diagram. A 8-nucleotide XmaI linker
was inserted into Stul site of the parental plasmid D46 to
construct the plasmid D46/1024. D46 is the complete antigenome cDNA
and is equivalent to D53; the difference in nomenclature is to
denote that these represent two different preparations. The
Xma-XmaI fragment of the plasmid 6196 was inserted into the plasmid
D46/1024 to construct the plasmid D46/1024CAT. The RNA encoded by
the D46cDNA is shown at the bottom, including the three 5'-terminal
nonviral G residues contributed by the T7 promoter and the
3'-terminal phosphorylated U residue contributed by cleavage of the
hammerhead ribozyme; the nucleotide lengths given for the
antigenome do not include these nonviral nucleotides. The L gene is
drawn offset to indicate the gene overlap.
FIG. 7 is a diagram (not to scale) of the parental wild-type D46
plasmid encoding an RSV antigenome (top), and the D46/6368
derivative in which the SH gene has been deleted (bottom). The RSV
genes are shown as open rectangles with the GS and GE transcription
signals shown as filled boxes on the upstream and downstream ends,
respectively. The T7 phage promoter (left) and hammerhead ribozyme
and T7 terminators used to generate the 3' end of the RNA
transcript (right) are shown as small open boxes. The ScaI and PadI
fragment of D46 was replaced with a short synthetic fragment,
resulting in D46/6368. The sequence flanking the SH gene in D46,
and the sequence of the engineered region in D46/6368, are each
shown framed in a box over the respective plasmid map (the top and
bottom lines of nucleotides represent sequences 4183-4240 and
4611-4691 of SEQ ID NO: 1, respectively). The sequence of the
ScaI-PacI fragment in D46, and its replacement in D46/6368, are
shown in bold and demarcated with arrows facing upward. The M GE,
SH GS, SH GE and G GS sites are indicated with overlining. The new
M-G intergenic region in D46/6368 is labeled 65 in the diagram at
the bottom to indicate its nucleotide length. The positive-sense T7
transcript of the SH-minus D46/6368 construct is illustrated at the
bottom; the three 5'-terminal nonviral G residues contributed by
the T7 promoter and the 3'-terminal U residue are shown (Collins,
et al. Proc. Natl. Acad. Sci. USA 92:11563-11567 (1995),
incorporated herein by reference). These nonviral nucleotides are
not included in length measurements.
FIG. 8 provides results of RT-PCR analysis of total intracellular
RNA from cells infected with the D46 wild-type or D46/6368 SH-minus
virus to confirm the deletion in the SH locus. RT was performed
with a positive-sense primer that anneals upstream of the SH gene,
and the PCR employed in addition a negative-sense primer that
anneals downstream of the SH gene. Lanes: (1 and 5) markers
consisting of the 1 Kb DNA ladder (Life Technologies, Gaithersburg,
Md.); (2) D46/6368 RNA subjected to RT-PCR; (3) D46 RNA subjected
to RT-PCR; (4) D46/6368 RNA subjected to PCR alone. PCR products
were electrophoresed on a 2.5% agarose gel and stained with
ethidium bromide. Nucleotides lengths of some marker DNA fragments
are shown to the right.
FIG. 9 shows Northern blot hybridization of RNAs encoded by the D46
wild-type and D46/6368 SH-minus virus. Total intracellular RNA was
isolated from infected cells and subjected to oligo(dT)
chromatography without a prior denaturation step, conditions under
which the selected RNA also includes genomic RNA due to sandwich
hybridization. RNAs were electrophoresed on formaldehyde-agarose
gels and blotted onto nitrocellulose membrane. Replicate blots were
hybridized individually with [.sup.32P]-labeled DNA probes of the
M, SH, G, F, M2, or L genes, as indicated. Lanes: (1) D46/6368 RNA;
(2) D46 RNA; (3) uninfected HEp-2 cell RNA. Positions of the
genomic RNA (gen.), mRNAs (large letters) and read-through
transcripts (small letters) are shown on the left. The positions of
the read-through transcripts P-M and M-G (M probe) coincide, as
well as the positions of G-F and F-M2 transcripts (F probe). The
positions of the 0.24-9.5 kb RNA ladder molecular weight markers
(Life Technologies), which was run in parallel and visualized by
hybridization with [.sup.32P]-labeled DNA of phage lambda, are
shown on the right.
FIG. 10 shows SDS-PAGE of [.sup.35S]-labeled RSV proteins
synthesized in HEp-2 cells infected with the D46 wild-type or
D46/6368 SH-minus virus. Proteins were subjected to
immunoprecipitation with antiserum raised against purified virions
and analyzed by electrophoresis in pre-cast gradient 4%-20%
Tris-glycine gels (Novex, San Diego, Calif.). Positions of viral
proteins are indicated to the left; positions and molecular masses
(in kilodaltons) of marker proteins (Kaleidoscope Prestained
Standards, Bio-Rad, Richmond, Calif.), are shown to the right.
FIGS. 11-13 provide growth curves for D46 wild-type and D46/6368
SH-minus viruses in HEp-2 cells (FIG. 11), 293 cells (FIG. 12), and
AGMK-21 cells (FIG. 13). Triplicate cell monolayers in 25-cm.sup.2
culture flasks were infected with 2 PFU per cell of either virus,
and incubated at 37.degree. C. Aliquots were taken at indicated
time points, stored at -70.degree. C., and titrated in parallel by
plaque assay with antibody staining. Each point shown is the
average titer of three infected cell monolayers.
FIGS. 14 and 15 show kinetics of virus replication in the upper
(FIG. 14) and lower (FIG. 15) respiratory tract of mice inoculated
intranasally with the D46 wild-type virus, D46/6368 SH-minus virus,
or the biologically-derived cpts248/404 virus. Mice in groups of 24
were inoculated intranasally with 10.sup.6 PFU of the indicated
virus. Six mice from each group were sacrificed on the indicated
day and the nasal turbinates and lung tissues were removed and
homogenized, and levels of infectious virus were determined by
plaque assay on individual specimens and mean log.sub.10 titers
were determined.
FIG. 16 shows a comparison of the transcription products and gene
order of SH-minus virus compared to its wild-type counterpart. The
upper panel summarizes an analysis of the amounts of certain mRNAs
produced by the SH-minus virus compared with the wild-type parent
recombinant virus. Intracellular mRNAs were isolated from cells
infected with the SH-minus or wild-type virus and analyzed by
Northern blot hybridization with gene-specific probes. The amount
of hybridized radioactivity was quantitated, and the relative
abundance of each individual mRNA produced by the SH-minus virus
versus its wild-type parent is shown. The lower panel shows the
gene order of the wild-type virus from the M gene (position 5 in
the gene order) to the L gene (position 10). This is compared to
that of the SH-minus virus, in which the positions in the gene
order of the G, F, M2 and L genes are altered due to deletion of
the SH gene.
FIG. 17 depicts the D46 antigenome plasmid which was modified by
deletion of the SH gene in such a way as to not insert any
heterologous sequence into the recombinant virus. The sequence
flanking the SH gene depicted at the top. The MGE, M-SH intergenic
(IG), SH GS, SH GE and SH-G IG sequences are shown. The area which
was removed by the deletion is underlined, with the deletion points
indicated with upward pointing triangles. The described nucleotide
segment consists of sequences 4198-4643 of SEQ ID NO: 1. The
antigenome resulting from this deletion is D46/6340.
FIG. 18 depicts the introduction of tandem translation stop codons
into the translational open reading frame (ORF) encoding the NS2
protein. Plasmid D13 contains the left end of the antigenome cDNA,
including the T7 promoter (shaded box), the leader region, and the
NS1, NS2, N, P, M and SH genes. Only the cDNA insert of D13 is
shown. The AatII-AflII fragment containing the T7 promoter and NS1
and NS2 genes was subcloned into a pGem vector, and site-directed
mutagenesis was used to modify the NS2 ORF in the region
illustrated by the sequence. The wild-type sequence of codons 18 to
26 (SEQ ID NO: 27) is shown (the encoded amino acids are indicated
below(SEQ ID NO: 28)), and the three nucleotides above are the
three substitutions which were made to introduce two termination
codons (ter) and an Xhal site (underlined) as a marker. The
resulting cDNA and subsequent recovered virus are referred to as
NS2-knockout (KO).
FIG. 19 compares production of infectious virus by wild-type RSV
(D53) versus NS2-knockout RSV in HEp-2 cells. Triplicate monolayers
were infected with either virus at an input moi of three pfu/cell,
and samples were taken at the indicated intervals and quantitated
by plaque assay and immunostaining.
FIG. 20 depicts alteration of gene-end (GE) signals of the NS1 and
NS2 genes. The cDNA insert of plasmid D13, representing the left
hand end of the antigenome cDNA from the T7 promoter (shaded) to
the Pad site at position 4623, is shown. The AatI-AflII fragment
containing the T7 promoter and the NS1 and NS2 genes was subcloned
into a pGem vector. It was modified by site-directed mutagenesis
simultaneously at two sites, namely the NS1 and NS2 GE signals were
each modified to be identical to that found in nature for the N
gene. The sequences of the wild-type NS1 (SEQ ID NO: 29) and NS2
(SEQ ID NO: 30) GE signals are shown (and identified by sequence
position relative to the complete antigenome sequence of SEQ ID NO:
1), and the nucleotide substitutions are shown above the line (SEQ
ID NOs: 31 and 32, respectively). The dash in the wildtype sequence
of the NS2 GE signal indicates that the mutation increased the
length of the GE signal by one nucleotide.
FIG. 21 depicts the deletion of the polynucleotide sequence
encoding the NS1protein. The left hand part of the D13 cDNA is
shown at the bottom: D13 contains the left hand part of the
antigenome cDNA, from the leader to the end of the SH gene, with
the T7promoter immediately upstream of the leader. The sequence on
either side of the deletion point (upward arrow) is shown on top;
nucleotide numbering corresponds to that of SEQ ID NO:1. The
deletion spans from immediately before the translational start site
of the NS1 ORF to immediately before that of the NS2 ORF. Thus, it
has the effect of fusing the NS1 GS and upstream noncoding region
to the N52 ORF. This precludes the disruption of any cis-acting
sequence elements which might extend into the NS1 gene due to its
leader-proximal location.
FIG. 22 depicts the deletion of the polynucleotide sequence
encoding the NS2mRNA. As described above, the left hand part of the
D13 cDNA is shown along with the sequence on either side of the
deletion point (upward arrow); nucleotide numbering corresponds to
that of SEQ ID NO:1. The deletion spans from immediately downstream
of the NS1 gene to immediately downstream of the NS2 gene. Thus,
the sequence encoding the NS2 mRNA has been deleted in its
entirety, but no other sequence has been disrupted. The resulting
cDNA and subsequent recovered recombinant virus are referred to as
.DELTA.NS2.
FIG. 23 depicts the ablation of the translational start site for
the secreted form of the G protein. The 298-amino acid G protein is
shown as an open rectangle with the signal-anchor sequence filled
in. The amino acid sequence for positions 45 to 53 (SEQ ID NO: 33)
is shown overhead to illustrate two nucleotide substitutions (SEQ
ID NO: 34) which change amino acid 48 from methionine to isoleucine
and amino acid 49 from isoleucine to valine. The former mutation
eliminates the translational start site for the secreted form. The
two mutations also create an MfeI site, which provides a convenient
method for detecting the mutation. The resulting cDNA and
subsequent recovered virus are referred to as M48I (methionine-48
to isoleucine-48).
FIG. 24 shows the results of a comparison of production of
infectious virus by wild-type RSV (D53) versus that of two isolates
of recovered D53/M481 membrane G mutant virus.
FIG. 25A shows the negative-sense genomic RNA of RSV strain A2
(antigenic subgroup A) and illustrates replacement of the F and G
genes with their counterparts of strain B1 (antigenic subgroup B).
Each rectangle represents a gene encoding a single mRNA, and the
grey and filled boxes at the left and right ends of each rectangle
represent gene-start (GS) and gene-end (GE) transcription signals,
respectively. The thin lines at each end of the genome represent
the leader (left end) and trailer (right end) extragenic regions,
and the thin lines between rectangles represent intergenic regions.
The gene replacement is done at the level of an antigenome cDNA
using PacI and SphI sites which precede the G gene and follow the F
gene, respectively. The L gene is drawn offset to illustrate that
it overlaps with the upstream M2 gene, a detail which is not
immediately germane to this example.
FIGS. 25B and 25C illustrate the sequence (positive-sense) in the
chimeric rAB virus, namely recombinant RSV strain A2 in which the F
and G glycoprotein genes were replaced with those of strain B1. The
sequence shown contains part of the SH-G (Part B, SEQ ID NO: 35)
and F-M2 (Part C, SEQ ID NO: 36) junction. Sequence derived from
the strain A2 backbone is shown in lower case, and that from the
strain B1 donor is in upper case. The last A2-specific nucleotide
at the junction between the A2 and B1 sequence is numbered
according to the unmodified recombinant A2 genomic sequence. The SH
gene-end (GE) and F GE signals are boxed. The PacI and SphI
recognition sites are italicized. IG: intergenic region.
FIG. 26 illustrates modification the cDNA of the strain B1 G and F
genes in order to improve stability during growth in E. coli. Two
positive-sense sequences are shown: the upper one (labeled "new")
is the modified B1 sequence (SEQ ID NO: 37), and the lower ("wt")
is the wild-type B1 sequence (nucleotides 5554-5663 of SEQ ID NO:
2). The sequence shown includes the downstream end of the G
translational open reading frame (ORF), its encoded amino acids
(shown as the single letter code below the sequence, SEQ ID NO:
38), the G GE signal (boxed), the G-F intergenic region, and the F
gene-start (GS) signal (boxed). Underlined positions in the new
sequence represent substitutions; dashes in the new sequence
represent deletions; dashes in the wt sequence indicate an
insertion in the new sequence. An MfeI site created in the new
sequence is in bold italics. A 47-nucleotide sequence from the G-F
intergenic region which was deleted in creating the new sequence is
indicated.
FIG. 27 illustrates replication of the chimeric recombinant AB wt
RSV and ABcp248/404/1030 derivative in the upper (top panel;
nasopharyngeal swab) and lower (lower panel; tracheal lavage)
respiratory tract of seronegative chimpanzees. This is based on
data from Table 46. The light horizontal dotted line in each graph
is the lower limit of detectability. Bars indicate Standard
Error.
DESCRIPTION OF THE SPECIFIC EMBODIMENTS
The present invention provides infectious, chimeric respiratory
syncytial virus (RSV) that are attenuated and capable of eliciting
a propylactic or therapeutic immune response in mammalian patients
susceptible to RSV infection. Also provided within the invention
are novel methods and compositions for designing and producing
attenuated, chimeric RSV, as well as methods and compositions for
prophylaxis and treatment of RSV infection.
Chimeric RSV of the invention are recombinantly engineered to
incorporate nucleotide sequences from more than one RSV strain or
subgroup to produce an infectious, chimeric virus or subviral
particle. In this manner, candidate vaccine virus are recombinantly
engineered to elicit an immune response against RSV in a mammalian
host, including humans and non-human primates. Chimeric RSV
according to the invention may elicit an immune response to a
specific RSV subgroup or strain, or they may elicit a polyspecific
response against multiple RSV subgroups or strains.
In exemplary embodiments of the invention, heterologous genes, gene
segments, or single or multiple nucleotides of one RSV are added to
a partial or complete RSV genome or antigenome or substituted
therein by counterpart sequence(s) from a heterologous RSV to
produce a chimeric RSV genome or antigenome. The chimeric RSV of
the invention thus includes a partial or complete "recipient" RSV
genome or antigenome from one RSV strain or subgroup virus combined
with an additional or replacement "donor" gene or gene segment of a
different RSV strain or subgroup virus.
In preferred aspects of the invention, chimeric RSV incorporate a
partial or complete human RSV genome or antigenome of one RSV
subgroup or strain combined with a heterologous gene or gene
segment from a different human RSV subgroup or strain. For example,
preferred chimeric RSV incorporate a chimeric genome or antigenome
comprised of a partial or complete human RSV A or B subgroup genome
or antigenome combined with a heterologous gene or gene segment
from a different human RSV A or B subgroup virus.
Heterologous donor genes or gene segments from one RSV strain or
subgroup are combined with or substituted within a recipient genome
or antigenome that serves as a backbone for insertion or addition
of the donor gene or gene segment. Thus, the recipient genome or
antigenome acts as a vector to import and express heterologous
genes or gene segments to yield chimeric RSV that exhibit novel
structural and/or phenotypic characteristics. Preferably, addition
or substitution of a heterologous gene or gene segment within a
selected recipient RSV strain yields novel phenotypic effects, for
example attenuation, growth changes, altered immunogenicity, or
other desired phenotypic changes, as compared with corresponding
phenotypes of the unmodified recipient and/or donor.
Genes and gene segments that are useful as heterologous inserts or
additions within a chimeric RSV genome or antigenome include genes
or gene segments encoding a NS1, NS2, N, P, M, SH, M2(ORF1),
M2(ORF2), L, F or G protein or a portion thereof. In preferred
embodiments invention, chimeric RSV incorporate a heterologous gene
encoding a RSV F, G or SH glycoprotein. Alternatively, the chimeric
RSV may incorporate a gene segment encoding only a portion of a
selected protein, for example a cytoplasmic domain, transmembrane
domain, ectodomain or immunogenic epitope of a RSV F, G or SH
glycoprotein.
In other embodiments, chimeric RSV useful in a vaccine formulation
can be conveniently modified to accommodate antigenic drift in
circulating virus. Typically the modification will be in the G
and/or F proteins. An entire G or F gene, or a gene segment
encoding a particular immunogenic region thereof, from one RSV
strain is incorporated into a chimeric RSV genome or antigenome
cDNA by replacement of a corresponding region in a recipient clone
of a different RSV strain or subgroup, or by adding one or more
copies of the gene, such that several antigenic forms are
represented. Progeny virus produced from the modified RSV clone can
then be used in vaccination protocols against emerging RSV
strains.
Thus, the introduction of heterologous immunogenic proteins,
domains and epitopes to produce chimeric RSV is particularly useful
to generate novel immune responses in an immunized host. Addition
or substitution of an immunogenic gene or gene segment from one,
donor RSV subgroup or strain within a recipient genome or
antigenome of a different RSV subgroup or strain can generate an
immune response directed against the donor subgroup or strain, the
recipient subgroup or strain, or against both the donor and
recipient subgroup or strain. To achieve this purpose, chimeric RSV
may also be constructed that express a chimeric protein, e.g., an
immunogenic protein having a cytoplasmic tail and/or transmembrane
domain specific to one RSV strain or subgroup fused to an
ectodomain of a different RSV. Other exemplary recombinants of this
type may express duplicate protein regions, such as duplicate
immunogenic regions.
Although it is often useful to add or substitute entire genes
(including cis-acting elements and coding regions) within a
chimeric genome or antigenome, it is also useful to transfer only a
portion of a donor gene of interest. Quite commonly, non-coding
nucleotides such as cis-acting regulatory elements and intergenic
sequences need not be transferred with the donor gene coding
region. In addition, a variety of gene segments provide useful
donor polynucleotides for inclusion within a chimeric genome or
antigenome to express chimeric RSV having novel and useful
properties. Thus, heterologous gene segments may beneficially
encode a cytoplasmic tail, transmembrane domain or ectodomain, an
epitopic site or region, a binding site or region, an active site
or region containing an active site, etc., of a selected protein
from one RSV. These and other gene segments can be added or
substituted for a counterpart gene segment in another RSV to yield
novel chimeric recombinants, for example recombinants expressing a
chimeric protein having a cytoplasmic tail and/or transmembrane
domain of one RSV fused to an ectodomain of another RSV. Useful
genome segments in this regard range from about 15-35 nucleotides
in the case of gene segments encoding small functional domains of
proteins, e.g., epitopic sites, to about 50, 75, 100, 200-500, and
500-1,500 or more nucleotides for gene segments encoding larger
domains or protein regions.
To construct chimeric RSV, heterologous genes may be added or
substituted in whole or in part to a background genome or
antigenome to form a chimeric genome or antigenome. In the case of
chimeras generated by substitution, a selected protein or protein
region (e.g., a cytoplasmic tail, transmembrane domain or
ectodomain, an epitopic site or region, a binding site or region,
an active site or region containing an active site, etc.) from one
RSV is substituted for a counterpart gene or gene segment in a
different RSV genome or antigenome to yield novel recombinants
having desired phenotypic changes compared to wild-type or parent
RSV strains. As used herein, "counterpart" genes, gene segments,
proteins or protein regions two counterpart polynucleotides from a
heterologous source, including different genes in a single RSV
strain, or different variants of the same gene, including species
and allelic variants among different RSV subgroups or strains.
Counterpart genes and gene segments share at least moderate
structural similarity. For example counterpart gene segments may
encode a common structural domain of a protein of interest, such as
a cytoplasmic domain, transmembrane domain, ectodomain, binding
site or region, epitopic site or region, etc. Typically, they will
share a common biological function as well. For example, protein
domains encoded by counterpart gene segments may providing a common
membrane spanning function, a specific binding activity, an
immunological recognition site, etc. Typically, a desired
biological activity shared between the products of counterpart
genes and gene segments will be substantially similar in
quantitative terms, i.e., they will not differ by more than 30%,
preferably by no more than 20%, more preferably by no more than
5-10%.
Counterpart genes and gene segments for use within the invention
embrace an assemblage of alternate species having a range of size
and sequence variation. However, selection of counterpart genes and
gene segments relies on substantial sequence identity between the
subject counterparts. In this context, a selected polynucleotide
"reference sequence" is defined as a sequence or portion thereof
present in either the donor or recipient genome or antigenome. This
reference sequence is used as a defined sequence to provide a
rationale basis for a sequence comparison. For example, the
reference sequence may be a defined a segment of a cDNA or gene, or
a complete cDNA or gene sequence.
Generally, a reference sequence for use in defining counterpart
genes and gene segments is at least 20 nucleotides in length,
frequently at least 25 nucleotides in length, and often at least 50
nucleotides in length. Since two polynucleotides may each (1)
comprise a sequence (i.e., a portion of the complete polynucleotide
sequence) that is similar between the two polynucleotides, and (2)
may further comprise a sequence that is divergent between the two
polynucleotides, sequence comparisons between two (or more)
polynucleotides are typically performed by comparing sequences of
the two polynucleotides over a "comparison window" to identify and
compare local regions of sequence similarity. A "comparison
window", as used herein, refers to a conceptual segment of at least
20 contiguous nucleotide positions wherein a polynucleotide
sequence may be compared to a reference sequence of at least 20
contiguous nucleotides and wherein the portion of the
polynucleotide sequence in the comparison window may comprise
additions or deletions (i.e., gaps) of 20 percent or less as
compared to the reference sequence (which does not comprise
additions or deletions) for optimal alignment of the two sequences.
Optimal alignment of sequences for aligning a comparison window may
be conducted by the local homology algorithm of Smith &
Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment
algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970),
by the search for similarity method of Pearson & Lipman, Proc.
Natl. Acad. Sci. USA 85:2444 (1988) (each of which is incorporated
by reference), by computerized implementations of these algorithms
(GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software
Package Release 7.0, Genetics Computer Group, 575 Science Dr.,
Madison, Wis., incorporated herein by reference), or by inspection,
and the best alignment (i.e., resulting in the highest percentage
of sequence similarity over the comparison window) generated by the
various methods is selected.
The term "sequence identity" as used herein means that two
polynucleotide sequences are identical (i.e., on a
nucleotide-by-nucleotide basis) over the window of comparison. The
term "percentage of sequence identity" is calculated by comparing
two optimally aligned sequences over the window of comparison,
determining the number of positions at which the identical nucleic
acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to
yield the number of matched positions, dividing the number of
matched positions by the total number of positions in the window of
comparison (i.e., the window size), and multiplying the result by
100 to yield the percentage of sequence identity. The terms
"substantial identity" as used herein denotes a characteristic of a
polynucleotide sequence, wherein the polynucleotide comprises a
sequence that has at least 85 percent sequence identity, preferably
at least 90 to 95 percent sequence identity, more usually at least
99 percent sequence identity as compared to a reference sequence
over a comparison window of at least 20 nucleotide positions,
frequently over a window of at least 25-50 nucleotides, wherein the
percentage of sequence identity is calculated by comparing the
reference sequence to the polynucleotide sequence which may include
deletions or additions which total 20 percent or less of the
reference sequence over the window of comparison. The reference
sequence may be a subset of a larger sequence.
In addition to these polynucleotide sequence relationships,
proteins and protein regions encoded by chimeric RSV of the
invention are also typically selected to have conservative
relationships, i.e., to have substantial sequence identity or
sequence similarity, with selected reference polypeptides. As
applied to polypeptides, the term "sequence identity" means
peptides share identical amino acids at corresponding positions.
The term "sequence similarity" means peptides have identical or
similar amino acids (i.e., conservative substitutions) at
corresponding positions. The term "substantial sequence identity"
means that two peptide sequences, when optimally aligned, such as
by the programs GAP or BESTFIT using default gap weights, share at
least 80 percent sequence identity, preferably at least 90 percent
sequence identity, more preferably at least 95 percent sequence
identity or more (e.g., 99 percent sequence identity). The term
"substantial similarity" means that two peptide sequences share
corresponding percentages of sequence similarity.
Preferably, residue positions which are not identical differ by
conservative amino acid substitutions. Conservative amino acid
substitutions refer to the interchangeability of residues having
similar side chains. For example, a conservative group of amino
acids having aliphatic side chains is glycine, alanine, valine,
leucine, and isoleucine; a group of amino acids having
aliphatic-hydroxyl side chains is serine and threonine; a group of
amino acids having amide-containing side chains is asparagine and
glutamine; a group of amino acids having aromatic side chains is
phenylalanine, tyrosine, and tryptophan; a group of amino acids
having basic side chains is lysine, arginine, and histidine; and a
group of amino acids having sulfur-containing side chains is
cysteine and methionine. Preferred conservative amino acids
substitution groups are: valine-leucine-isoleucine,
phenylalanine-tyrosine, lysine-arginine, alanine-valine, and
asparagine-glutamine. Stereoisomers (e.g., D-amino acids) of the
twenty conventional amino acids, unnatural amino acids such as
.alpha.,.alpha.-disubstituted amino acids, N-alkyl amino acids,
lactic acid, and other unconventional amino acids may also be
suitable components for polypeptides of the present invention.
Examples of unconventional amino acids include: 4-hydroxyproline,
.gamma.-carboxyglutamate, .epsilon.-N,N,N-trimethyllysine,
.epsilon.-N-acetyllysine, O-phosphoserine, N-acetylserine,
N-formylmethionine, 3-methylhistidine, 5-hydroxylysine,
.omega.-N-methylarginine, and other amino and imino acids (e.g.,
4-hydroxyproline). Moreover, amino acids may be modified by
glycosylation, phosphorylation and the like.
The invention disclosed herein describes cDNA-based methods that
are useful to construct a large panel of recombinant, chimeric RSV
viruses and subviral particles. These recombinant constructs offer
improved characteristics of attenuation and immunogenicity for use
as vaccine agents. Among desired phenotypic changes in this context
are resistance to reversion from an attenuated phenotype,
improvements in attenuation in culture or in a selected host
environment, immunogenic characteristics (e.g., as determined by
enhancement, or diminution, of an elicited immune response),
upregulation or downregulation of transcription and/or translation
of selected viral products, etc.
In one preferred aspect of the invention, attenuated, chimeric RSV
are produced in which the chimeric genome or antigenome is further
modified by introducing one or more attenuating point mutations
that specifies an attenuating phenotype. These point mutations may
be generated de novo and tested for attenuating effects according
to a rational design mutagenesis strategy. Alternatively, the
attenuating point mutations are identified in biologically derived
mutant RSV and thereafter incorporated into a chimeric RSV of the
invention.
Attenuating point mutations in biologically derived RSV for
incorporation within a chimeric vaccine strain may occur naturally
or may be introduced into wild-type RSV strains by well known
mutagenesis procedures. For example, incompletely attenuated
parental RSV strains can be produced by chemical mutagenesis during
virus growth in cell cultures to which a chemical mutagen has been
added, by selection of virus that has been subjected to passage at
suboptimal temperatures in order to introduce growth restriction
mutations, or by selection of a mutagenized virus that produces
small plaques (sp) in cell culture, as generally described herein
and in U.S. Ser. No. 08/327,263, incorporated herein by
reference.
By "biologically derived RSV" is meant any RSV not produced by
recombinant means. Thus, biologically derived RSV include naturally
occurring RSV of all subgroups and strains, including, e.g.,
naturally occurring RSV having a wild-type genomic sequence and RSV
having genomic variations from a reference wild-type RSV sequence,
e.g., RSV having a mutation specifying an attenuated phenotype.
Likewise, biologically derived RSV include RSV mutants derived from
a parental RSV strain by, inter alia, artificial mutagenesis and
selection procedures.
To produce a satisfactorily attenuated RSV from biologically
derived strains, mutations are preferably introduced into a
parental strain which has been incompletely or partially
attenuated, such as the well known ts-1 or ts-1NG or cpRSV mutants
of the A2 strain of RSV subgroup A, or derivatives or subclones
thereof. Using these and other partially attenuated strains
additional mutation(s) can be generated that further attenuate the
strain, e.g., to a desired level of restricted replication in a
mammalian host, while retaining sufficient immunogenicity to confer
protection in vaccinees.
Partially attenuated mutants of the subgroup A or B virus can be
produced by well known methods of biologically cloning wild-type
virus in an acceptable cell substrate and developing, e.g.,
cold-passaged mutants thereof, subjecting the virus to chemical
mutagenesis to produce ts mutants, or selecting small plaque or
similar phenotypic mutants (see, e.g., Murphy et al., International
Publication WO 93/21310, incorporated herein by reference). For
virus of subgroup B, an exemplary, partially attenuated parental
virus is cp 23, which is a mutant of the B1 strain of subgroup
B.
Various known selection techniques may be combined to produce
partially attenuated mutants from non-attenuated subgroup A or B
strains which are useful for further derivatization as described
herein. Further, mutations specifying attenuated phenotypes may be
introduced individually or in combination in incompletely
attenuated subgroup A or B virus to produce vaccine virus having
multiple, defined attenuating mutations that confer a desired level
of attenuation and immunogenicity in vaccinees.
As noted above, production of a sufficiently attenuated
biologically derived RSV mutant can be accomplished by several
known methods. On such procedure involves subjecting a partially
attenuated virus to passage in cell culture at progressively lower,
attenuating temperatures. For example, whereas wild-type virus is
typically cultivated at about 34-37.degree. C., the partially
attenuated mutants are produced by passage in cell cultures (e.g.,
primary bovine kidney cells) at suboptimal temperatures, e.g.,
20-26.degree. C. Thus, the cp mutant or other partially attenuated
strain, e.g., ts-1 or spRSV, is adapted to efficient growth at a
lower temperature by passage in MRC-5 or Vero cells, down to a
temperature of about 20-24.degree. C., preferably 20-22.degree. C.
This selection of mutant RSV during cold-passage substantially
eliminates any residual virulence in the derivative strains as
compared to the partially attenuated parent.
Alternatively, specific mutations can be introduced into
biologically derived RSV by subjecting a partially attenuated
parent virus to chemical mutagenesis, e.g., to introduce ts
mutations or, in the case of viruses which are already ts,
additional ts mutations sufficient to confer increased attenuation
and/or stability of the ts phenotype on the attenuated derivative.
Means for the introduction of ts mutations into RS virus include
replication of the virus in the presence of a mutagen such as
5-fluorouridine or 5-fluorouracil in a concentration of about
10.sup.-3 to 10.sup.-5 M, preferably about 10.sup.-4 M, exposure of
virus to nitrosoguanidine at a concentration of about 100 .mu.g/ml,
according to the general procedure described in, e.g., Gharpure et
al., J. Virol. 3:414-421 (1969) and Richardson et al., J. Med.
Virol. 3:91-100 (1978), or genetic introduction of specific ts
mutations. Other chemical mutagens can also be used. Attenuation
can result from a ts mutation in almost any RSV gene, although a
particularly amenable target for this purpose has been found to be
the polymerase (L) gene.
The level of temperature sensitivity of replication in exemplary
attenuated RSV for use within the invention is determined by
comparing its replication at a permissive temperature with that at
several restrictive temperatures. The lowest temperature at which
the replication of the virus is reduced 100-fold or more in
comparison with its replication at the permissive temperature is
termed the shutoff temperature. In experimental animals and humans,
both the replication and virulence of RSV correlate with the
mutant's shutoff temperature. Replication of mutants with a shutoff
temperature of 39.degree. C. is moderately restricted, whereas
mutants with a shutoff of 38.degree. C. replicate less well and
symptoms of illness are mainly restricted to the upper respiratory
tract. A virus with a shutoff temperature of 35 to 37.degree. C.
will typically be fully attenuated in humans. Thus, attenuated
biologically derived mutant and chimeric RSV of the invention which
are ts will have a shutoff temperature in the range of about 35 to
39.degree. C., and preferably from 35 to 38.degree. C. The addition
of a ts mutation into a partially attenuated strain produces
multiply attenuated virus useful within vaccine compositions of the
invention.
A number of attenuated RSV strains as candidate vaccines for
intranasal administration have been developed using multiple rounds
of chemical mutagenesis to introduce multiple mutations into a
virus which had already been attenuated during cold-passage (e.g.,
Connors et al., Virology 208: 478-484 (1995); Crowe et al., Vaccine
12: 691-699 (1994); and Crowe et al., Vaccine 12: 783-790 (1994),
incorporated herein by reference). Evaluation in rodents,
chimpanzees, adults and infants indicate that certain of these
candidate vaccine strains are relatively stable genetically, are
highly immunogenic, and may be satisfactorily attenuated.
Nucleotide sequence analysis of some of these attenuated viruses,
as exemplified hereinbelow, indicates that each level of increased
attenuation is associated with specific nucleotide and amino acid
substitutions. The present invention provides the ability to
distinguish between silent incidental mutations versus those
responsible for phenotype differences by introducing the mutations,
separately and in various combinations, into the genome or
antigenome of infectious RSV clones. This process coupled with
evaluation of phenotype characteristics of parental and derivative
virus identifies mutations responsible for such desired
characteristics as attenuation, temperature sensitivity,
cold-adaptation, small plaque size, host range restriction,
etc.
Mutations thus identified are compiled into a "menu" and are then
introduced as desired, singly or in combination, to calibrate a
chimeric vaccine virus to an appropriate level of attenuation,
immunogenicity, genetic resistance to reversion from an attenuated
phenotype, etc., as desired. Preferably, chimeric RSV of the
invention are attenuated by incorporation of at least one, and more
preferably two or more, attenuating point mutations identified from
such a menu, which may be defined as a group of known mutations
within a panel of biologically derived mutant RSV strains.
Preferred panels of mutant RSV strains described herein are cold
passaged (cp) and/or temperature sensitive (ts) mutants, for
example a panel comprised of RSV mutants designated "cpts RSV 248
(ATCC VR 2450), cpts RSV 248/404 (ATCC VR 2454), cpts RSV 248/955
(ATCC VR 2453), cpts RSV 530 (ATCC VR 2452), cpts RSV 530/1009
(ATCC VR 2451), cpts RSV 530/1030 (ATCC VR 2455), RSV B-1 cp52/2B5
(ATCC VR 2542), and RSV B-1 cp-23 (ATCC VR 2579)" (each deposited
under the terms of the Budapest Treaty with the American Type
Culture Collection (ATCC) of 10801 University Boulevard, Manassas,
Va. 20110-2209, U.S.A., and granted the above identified accession
numbers).
From this exemplary panel of biologically derived mutants, a large
menu of attenuating mutations are provided which can each be
combined with any other mutation(s) within the panel for
calibrating the level of attenuation in a recombinant, chimeric RSV
for vaccine use. Additional mutations may be derived from RSV
having non-ts and non-cp attenuating mutations as identified, e.g.,
in small plaque (sp), cold-adapted (ca) or host-range restricted
(hr) mutant strains. Attenuating mutations may be selected in
coding portions of a donor or recipient RSV gene or in non-coding
regions such as a cis-regulatory sequence. For example, attenuating
mutations may include single or multiple base changes in a gene
start sequence, as exemplified by a single or multiple base
substitution in the M2 gene start sequence at nucleotide 7605.
Chimeric RSV designed and selected for vaccine use often have at
least two and sometimes three or more attenuating mutations to
achieve a satisfactory level of attenuation for broad clinical use.
In one embodiment, at least one attenuating mutation occurs in the
RSV polymerase gene (either in the donor or recipient gene) and
involves a nucleotide substitution specifying an amino acid change
in the polymerase protein specifying a temperature-sensitive (ts)
phenotype. Exemplary chimeric RSV in this context incorporate one
or more nucleotide substitutions in the large polymerase gene L
resulting in an amino acid change at amino acid Phe.sub.521,
Gln.sub.831, Met.sub.1169, or Tyr.sub.1321, as exemplified by the
changes, Leu for Phe.sub.521, Leu for Gln.sub.831, Val for
Met.sub.1169, and Asn for Tyr.sub.1321. Alternately or
additionally, chimeric RSV of the invention may incorporate a ts
mutation in a different RSV gene, e.g., in the M2 gene. Preferably,
two or more nucleotide changes are incorporated in a codon
specifying an attenuating mutation, e.g., in a codon specifying a
ts mutation, thereby decreasing the likelihood of reversion from an
attenuated phenotype.
In accordance with the methods of the invention, chimeric RSV can
be readily constructed and characterized that incorporate at least
one and up to a full complement of attenuating point mutations
present within a panel of biologically derived mutant RSV strains.
Thus, mutations can be assembled in any combination from a selected
panel of mutants, for example, cpts RSV 248 (ATCC VR 2450), cpts
RSV 248/404 (ATCC VR 2454), cpts RSV 248/955 (ATCC VR 2453), cpts
RSV 530 (ATCC VR 2452), cpts RSV 530/1009 (ATCC VR 2451), cpts RSV
530/1030 (ATCC VR 2455), RSV B-1 cp52/2B5 (ATCC VR 2542), and RSV
B-1 cp-23 (ATCC VR 2579). In this manner, attenuation of chimeric
vaccine candidates can be finely calibrated for use in one or more
classes of patients, including seronegative infants.
In more specific embodiments, chimeric RSV for vaccine use
incorporate at least one and up to a full complement of attenuating
mutations specifying a temperature-sensitive amino acid
substitution at Phe.sub.521, Gln.sub.831, Met.sub.1169 or
Tyr.sub.1321 in the RSV polymerase gene L, or a
temperature-sensitive nucleotide substitution in the gene-start
sequence of gene M2. Alternatively or additionally, chimeric RSV of
claim may incorporate at least one and up to a full complement of
mutations from cold-passaged attenuated RSV, for example one or
more mutations specifying an amino acid substitution at Val.sub.267
in the RSV N gene, Glu.sub.218 or Thr.sub.523 in the RSV F gene,
Cys.sub.319 or His.sub.1690 in the RSV polymerase gene L.
In other detailed embodiments, the chimeric RSV of the invention
features human RSV B subgroup glycoprotein genes F and G that are
added or substituted within a human RSV A genome or antigenome to
form a chimeric clone which is further modified to incorporate one
or more attenuating point mutations adopted from biologically
derived mutant RSV. In various examples, the chimeric RSV has both
human RSV B subgroup glycoprotein genes F and G are substituted to
replace counterpart F and G glycoprotein genes within an RSV A
genome, which is further modified to incorporate attenuating point
mutations selected from (i) a panel of mutations specifying
temperature-sensitive amino acid substitutions Gln.sub.831 to Leu,
and Tyr.sub.1321 to Asn in the RSV polymerase gene L; (ii) a
temperature-sensitive nucleotide substitution in the gene-start
sequence of gene M2; (iii) an attenuating panel of mutations
adopted from cold-passaged RSV specifying amino acid substitutions
Val.sub.267 Ile in the RSV N gene, and Cys.sub.319 to Tyr and
His.sub.1690 Tyr in the RSV polymerase gene L; or (iv) a deletion
of the SH gene. Preferably, these and other examples of chimeric
RSV incorporate at least two attenuating point mutations adopted
from biologically derived mutant RSV, which may be derived from the
same or different biologically derived mutant RSV strains. Also
preferably, these exemplary mutants have one or more of their
attenuating mutations stabilized by multiple nucleotide changes in
a codon specifying the mutation.
In accordance with the foregoing description, the ability to
produce infectious RSV from cDNA permits introduction of specific
engineered changes within chimeric RSV. In particular, infectious,
recombinant RSV are employed for identification of specific
mutation(s) in biologically derived, attenuated RSV strains, for
example mutations which specify ts, ca, att and other phenotypes.
Desired mutations are thus identified and introduced into
recombinant, chimeric RSV vaccine strains. The capability of
producing virus from cDNA allows for routine incorporation of these
mutations, individually or in various selected combinations, into a
full-length cDNA clone, whereafter the phenotypes of rescued
recombinant viruses containing the introduced mutations to be
readily determined.
By identifying and incorporating specific, biologically derived
mutations associated with desired phenotypes, e.g., a cp or ts
phenotype, into infectious chimeric RSV clones, the invention
provides for other, site-specific modifications at, or within close
proximity to, the identified mutation. Whereas most attenuating
mutations produced in biologically derived RSV are single
nucleotide changes, other "site specific" mutations can also be
incorporated by recombinant techniques into biologically derived or
recombinant RSV. As used herein, site-specific mutations include
insertions, substitutions, deletions or rearrangements of from 1 to
3, up to about 5-15 or more altered nucleotides (e.g., altered from
a wild-type RSV sequence, from a sequence of a selected mutant RSV
strain, or from a parent recombinant RSV clone subjected to
mutagenesis). Such site-specific mutations may be incorporated at,
or within the region of, a selected, biologically derived point
mutation. Alternatively, the mutations can be introduced in various
other contexts within an RSV clone, for example at or near a
cis-acting regulatory sequence or nucleotide sequence encoding a
protein active site, binding site, immunogenic epitope, etc.
Site-specific RSV mutants typically retain a desired attenuating
phenotype, but may exhibit substantially altered phenotypic
characteristics unrelated to attenuation, e.g., enhanced or
broadened immunogenicity, or improved growth. Further examples of
desired, site-specific mutants include recombinant RSV designed to
incorporate additional, stabilizing nucleotide mutations in a codon
specifying an attenuating point mutation. Where possible, two or
more nucleotide substitutions are introduced at codons that specify
attenuating amino acid changes in a parent mutant or recombinant
RSV clone, yielding a biologically derived or recombinant RSV
having genetic resistance to reversion from an attenuated
phenotype. In other embodiments, site-specific nucleotide
substitutions, additions, deletions or rearrangements are
introduced upstream (N-terminal direction) or downstream
(C-terminal direction), e.g, from 1 to 3, 5-10 and up to 15
nucleotides or more 5' or 3', relative to a targeted nucleotide
position, e.g., to construct or ablate an existing cis-acting
regulatory element.
In addition to single and multiple point mutations and
site-specific mutations, changes to chimeric RSV disclosed herein
include deletions, insertions, substitutions or rearrangements of
whole genes or gene segments. These mutations may alter small
numbers of bases (e.g., from 15-30 bases, up to 35-50 bases or
more), or large blocks of nucleotides (e.g., 50-100, 100-300,
300-500, 500-1,000 bases) in the donor or recipient genome or
antigenome, depending upon the nature of the change (i.e., a small
number of bases may be changed to insert or ablate an immunogenic
epitope or change a small gene segment, whereas large block(s) of
bases are involved when genes or large gene segments are added,
substituted, deleted or rearranged.
In additional aspects, the invention provides for supplementation
of mutations adopted into a chimeric RSV clone from biologically
derived RSV, e.g., cp and ts mutations, with additional types of
mutations involving the same or different genes in a further
modified chimeric RSV clone. RSV encodes ten mRNAs and ten or
eleven proteins. Three of these are transmembrane surface proteins,
namely the attachment G protein, fusion F protein involved in
penetration, and small hydrophobic SH protein. G and F are the
major viral neutralization and protective antigens. Four additional
proteins are associated with the viral nucleocapsid, namely the RNA
binding protein N, the phosphoprotein P, the large polymerase
protein L, and the transcription elongation factor M2 ORF1. The
matrix M protein is part of the inner virion and probably mediates
association between the nucleocapsid and the envelope. Finally,
there are two nonstructural proteins, NS1 and NS2, of unknown
function. These proteins can be selectively altered in terms of
expression levels, or can be added deleted, substituted or
rearranged, in whole or in part, alone or in combination, with
other desired modifications, to yield a chimeric RSV exhibiting
novel vaccine characteristics.
Thus, in addition to, or in combination with, attenuating mutations
adopted from biologically derived RSV mutants, the present
invention also provides a range of additional methods for
attenuating chimeric RSV based on recombinant engineering of
infectious RSV clones. In accordance with this aspect of the
invention, a variety of alterations can be produced in an isolated
polynucleotide sequence encoding the chimeric RSV genome or
antigenome for incorporation into infectious clones. More
specifically, to achieve desired structural and phenotypic changes
in chimeric RSV, the invention allows for introduction of
modifications which delete, substitute, introduce, or rearrange a
selected nucleotide or plurality of nucleotides from a parent
chimeric genome or antigenome, as well as mutations which delete,
substitute, introduce or rearrange whole gene(s) or gene
segment(s), within a chimeric RSV clone.
Desired modifications of infectious chimeric RSV are typically
selected to specify a desired phenotypic change, e.g., a change in
viral growth, temperature sensitivity, ability to elicit a host
immune response, attenuation, etc. These changes can be brought
about either in a donor or recipient genome or antigenome by, e.g.,
mutagenesis of a parent RSV clone to ablate, introduce or rearrange
a specific gene(s) or gene region(s) (e.g., a gene segment that
encodes a protein structural domain, such as a cytoplasmic,
transmembrane or extracellular domain, an immunogenic epitope,
binding region, active site, etc.). Genes of interest in this
regard include all of the genes of the RSV genome:
3'-NS1-NS2-N-P-M-SH-G-F-M2-L-5', as well as heterologous genes from
other RSV, other viruses and a variety of other non-RSV sources as
indicated herein.
Also provided are modifications in a chimeric RSV which simply
alter or ablate expression of a selected gene, e.g., by introducing
a termination codon within a selected RSV coding sequence, changing
the position of an RSV gene relative to an operably linked
promoter, introducing an upstream start codon to alter rates of
expression, modifying (e.g., by changing position, altering an
existing sequence, or substituting an existing sequence with a
heterologous sequence) GS and/or GE transcription signals to alter
phenotype (e.g., growth, temperature restrictions on transcription,
etc.), and various other deletions, substitutions, additions and
rearrangements that specify quantitative or qualitative changes in
viral replication, transcription of selected gene(s), or
translation of selected protein(s).
The ability to analyze and incorporate other types of attenuating
mutations into chimeric RSV for vaccine development extends to a
broad assemblage of targeted changes in RSV clones. For example,
deletion of the SH gene yields a recombinant RSV having novel
phenotypic characteristics, including enhanced growth. In the
present invention, an SH gene deletion (or any other selected,
non-essential gene or gene segment deletion), is combined in a
chimeric RSV with one or more additional mutations specifying an
attenuated phenotype, e.g., one or more point mutation(s) adopted
from a biologically derived attenuated RSV mutant. In exemplary
embodiments, the SH gene or NS2 gene is deleted in combination with
one or more cp and/or ts mutations adopted from cpts248/404,
cpts530/1009, cpts530/1030, or another selected mutant RSV strain,
to yield a recombinant RSV having increased yield of virus,
enhanced attenuation, and resistance to phenotypic reversion, due
to the combined effects of the different mutations.
In this regard, any RSV gene which is not essential for growth, for
example the SH, N, P, NS1 and NS2 genes, can be ablated or
otherwise modified in a chimeric RSV to yield desired effects on
virulence, pathogenesis, immunogenicity and other phenotypic
characters. For example, ablation by deletion of a non-essential
gene such as SH results in enhanced viral growth in culture.
Without wishing to be bound by theory, this effect is likely due in
part to a reduced nucleotide length of the viral genome. In the
case of one exemplary SH-minus clone, the modified viral genome is
14,825 nt long, 398 nucleotides less than wild-type. By engineering
similar mutations that decrease genome size, e.g., in other coding
or noncoding regions elsewhere in the RSV genome, such as in the P,
M, F and M2 genes, the invention provides several readily
obtainable methods and materials for improving chimeric RSV
growth.
In addition, a variety of other genetic alterations can be produced
in a RSV genome or antigenome for incorporation into infectious
chimeric RSV, alone or together with one or more attenuating point
mutations adopted from a biologically derived mutant RSV.
Additional heterologous genes and gene segments (e.g. from
different RSV genes, different RSV strains or types, or non-RSV
sources) may be inserted in whole or in part, the order of genes
changed, gene overlap removed, an RSV genome promoter replaced with
its antigenome counterpart, portions of genes removed or
substituted, and even entire genes deleted. Different or additional
modifications in the sequence can be made to facilitate
manipulations, such as the insertion of unique restriction sites in
various intergenic regions or elsewhere. Nontranslated gene
sequences can be removed to increase capacity for inserting foreign
sequences.
Also provided within the invention are genetic modifications in a
chimeric RSV which alter or ablate the expression of a selected
gene or gene segment without removing the gene or gene segment from
the chimeric RSV clone. For example, this can be achieved by
introducing a termination codon within a selected coding sequence,
changing the position of a gene or introducing an upstream start
codon to alter its rate of expression, or changing GS and/or GE
transcription signals to alter phenotype (e.g., growth, temperature
restrictions on transcription, etc.).
Preferred mutations in this context include mutations directed
toward cis-acting signals, which can be identified, e.g., by
mutational analysis of RSV minigenomes. For example, insertional
and deletional analysis of the leader and trailer and flanking
sequences identified viral promoters and transcription signals and
provided a series of mutations associated with varying degrees of
reduction of RNA replication or transcription. Saturation
mutagenesis (whereby each position in turn is modified to each of
the nucleotide alternatives) of these cis-acting signals also has
identified many mutations which reduced (or in one case increased)
RNA replication or transcription. Any of these mutations can be
inserted into a chimeric antigenome or genome as described
herein.
Evaluation and manipulation of trans-acting proteins and cis-acting
RNA sequences using the complete antigenome cDNA is assisted by the
use of RSV minigenomes (see, e.g., Grosfeld et al., J. Virol. 69:
5677-5686 (1995), incorporated herein by reference), whose
helper-dependent status is useful in the characterization of those
mutants which are too inhibitory to be recovered in
replication-independent infectious virus.
Other mutations within chimeric RSV of the present invention
involve replacement of the 3' end of genome with its counterpart
from antigenome, which is associated with changes in RNA
replication and transcription. In addition, the intergenic regions
(Collins et al., Proc. Natl. Acad. Sci. USA 83:4594-4598 (1986),
incorporated herein by reference) can be shortened or lengthened or
changed in sequence content, and the naturally-occurring gene
overlap (Collins et al., Proc. Natl. Acad. Sci. USA 84:5134-5138
(1987), incorporated herein by reference) can be removed or changed
to a different intergenic region by the methods described
herein.
In one exemplary embodiment, the level of expression of specific
RSV proteins, such as the protective F and G antigens, can be
increased by substituting the natural sequences with ones which
have been made synthetically and designed to be consistent with
efficient translation. In this context, it has been shown that
codon usage can be a major factor in the level of translation of
mammalian viral proteins (Haas et al., Current Biol. 6:315-324
(1996)). Examination of the codon usage of the mRNAs encoding the F
and G proteins of RSV, which are the major protective antigens,
shows that the usage is consistent with poor expression. Thus,
codon usage can be improved by the recombinant methods of the
invention to achieve improved expression for selected genes.
In another exemplary embodiment, a sequence surrounding a
translational start site (preferably including a nucleotide in the
-3 position) of a selected RSV gene is modified, alone or in
combination with introduction of an upstream start codon, to
modulate chimeric RSV gene expression by specifying up- or
down-regulation of translation.
Alternatively, or in combination with other RSV modifications
disclosed herein, chimeric RSV gene expression can be modulated by
altering a transcriptional GS signal of a selected gene(s) of the
virus. In one exemplary embodiment, the GS signal of NS2 is
modified to include a defined mutation (e.g., the 404(M2) mutation
described hereinbelow) to superimpose a ts restriction on viral
replication.
Yet additional chimeric RSV clones within the invention can
incorporate modifications to a transcriptional GE signal. For
example, RSV clones may be generated which have a substituted or
mutated GE signal of the NS1 and NS2 genes for that of the N gene,
resulting in decreased levels of readthrough mRNAs and increased
expression of proteins from downstream genes. The resulting
chimeric virus will exhibit increased growth kinetics and increased
plaque size, providing but one example of alteration of RSV growth
properties by modification of a cis-acting regulatory element in
the RSV genome.
In another exemplary embodiment, expression of the G protein is
increased by modification of the G mRNA. The G protein is expressed
as both a membrane bound and a secreted form, the latter form being
expressed by translational initiation at a start site within the G
translational open reading frame. The secreted form can account for
as much as one-half of the expressed G protein. Ablation of the
internal start site (e.g., by sequence alteration, deletion, etc.),
alone or together with altering the sequence context of the
upstream start site yields desired changes in G protein expression.
Ablation of the secreted form of G also will improve the quality of
the host immune response to exemplary, chimeric RSV, because the
soluble form of G is thought to act as a "decoy" to trap
neutralizing antibodies. Also, soluble G protein has been
implicated in enhanced immunopathology due to its preferential
stimulation of a Th2-biased response.
In alternative embodiments, levels of chimeric RSV gene expression
are modified at the level of transcription. In one aspect, the
position of a selected gene in the RSV gene map can be changed to a
more promoter-proximal or promotor-distal position, whereby the
gene will be expressed more or less efficiently, respectively.
According to this aspect, modulation of expression for specific
genes can be achieved yielding reductions or increases of gene
expression from two-fold, more typically four-fold, up to ten-fold
or more compared to wild-type levels. In one example, the NS2 gene
(second in order in the RSV gene map) is substituted in position
for the SH gene (sixth in order), yielding a predicted decrease in
expression of NS2. Increased expression of selected RSV genes due
to positional changes can be achieved up to 10-fold, 30-fold,
50-fold, 100-fold or more, often attended by a commensurate
decrease in expression levels for reciprocally, positionally
substituted genes.
In other exemplary embodiments, the F and G genes are
transpositioned singly or together to a more promoter-proximal or
promoter-distal site within the chimeric RSV gene map to achieve
higher or lower levels of gene expression, respectively. These and
other transpositioning changes yield novel chimeric RSV clones
having attenuated phenotypes, for example due to decreased
expression of selected viral proteins involved in RNA
replication.
In more detailed aspects of the invention, chimeric RSV is provided
in which expression of a viral gene, for example the NS2 gene, is
ablated at the translational level without deletion of the gene or
of a segment thereof, by, e.g., introducing two tandem
translational termination codons into a translational open reading
frame (ORF). This yields viable virus in which a selected gene has
been silenced at the level of translation, without deleting its
gene. These forms of "knock-out" virus will exhibit reduced growth
rates and small plaque sizes in tissue culture. Thus, the methods
and compositions of the invention provide yet additional, novel
types of attenuating mutations which ablate expression of a viral
gene that is not one of the major viral protective antigens. In
this context "knockout" virus phenotypes produced without deletion
of a gene or gene segment can be alternatively produced by deletion
mutagenesis, as described herein, to effectively preclude
correcting mutations that may restore synthesis of a target
protein.
Several other gene "knock-outs" for chimeric RSV can be made using
alternate designs. For example, insertion of translation
termination codons into ORFs, or disruption of the RNA editing
sites, offer alternatives to silencing or attenuating the
expression of selected genes. Methods for producing these and other
knock-outs are well known in the art (as described, for example, in
Kretzschmar et al., Virology 216:309-316 (1996); Radecke et al.,
Virology 217:418-412 (1996); and Kato et al., EMBO J. 16:178-587
(1987); and Schneider et al., Virology 277:314-322 (1996), each
incorporated herein by reference).
Infectious chimeric RSV clones of the invention can also be
engineered according to the methods and compositions disclosed
herein to enhance immunogenicity and induce a level of protection
greater than that provided by infection with a wild-type RSV or a
parent chimeric RSV. For example, an immunogenic epitope from a
heterologous RSV strain or type, or from a non-RSV source such as
PIV, can be added to a chimeric clone by appropriate nucleotide
changes in the polynucleotide sequence encoding the chimeric genome
or antigenome. Alternatively, chimeric RSV can be engineered to add
or ablate (e.g., by amino acid insertion, substitution or deletion)
immunogenic epitopes associated with desirable or undesirable
immunological reactions.
Within the methods of the invention, additional genes or gene
segments may be inserted into or proximate to the recipient RSV
genome or antigenome. These genes may be under common control with
recipient genes, or may be under the control of an independent set
of transcription signals. Genes of interest include the RSV genes
identified above, as well as non-RSV genes. Non-RSV genes of
interest include those encoding cytokines (e.g., IL-2 through
IL-15, especially IL-2, IL-6 and IL-12, etc.), gamma-interferon,
and proteins rich in T helper cell epitopes. These additional
proteins can be expressed either as a separate protein, or as a
chimera engineered from a second copy of one of the RSV proteins,
such as SH. This provides the ability to modify and improve the
immune responses against RSV both quantitatively and
qualitatively.
In exemplary embodiments of the invention, insertion of foreign
genes or gene segments, and in some cases of noncoding nucleotide
sequences, within a chimeric RSV genome results in a desired
increase in genome length causing yet additional, desired
phenotypic effects. Increased genome length results in attenuation
of the resultant RSV, dependent in part upon the length of the
insert. In addition, the expression of certain proteins, e.g. a
cytokine, from a non-RSV gene inserted into chimeric RSV of the
invention will result in attenuation of the virus due to the action
of the protein. This has been described for IL-2 expressed in
vaccinia virus (e.g. Flexner et al., Nature 33:-259-62 (1987)) and
is also expected for gamma interferon.
Deletions, insertions, substitutions and other mutations involving
changes of whole viral genes or gene segments within chimeric RSV
of the invention yield highly stable vaccine candidates, which are
particularly important in the case of immunosuppressed individuals.
Many of these changes will result in attenuation of resultant
vaccine strains, whereas others will specify different types of
desired phenotypic changes. For example, certain viral genes are
known which encode proteins that specifically interfere with host
immunity (see, e.g., Kato et al., EMBO. J. 16:578-87 (1997),
incorporated herein by reference). Ablation of such genes in
chimeric vaccine viruses is expected to reduce virulence and
pathogenesis and/or improve immunogenicity.
In alternative aspects of the invention, the infectious chimeric
RSV produced from a cDNA-expressed genome or antigenome can be any
of the RSV or RSV-like strains, e.g., human, bovine, murine, etc.,
or of any pneumovirus, e.g., pneumonia virus of mice or turkey
rhinotracheitis virus. To engender a protective immune response,
the RSV strain may be one which is endogenous to the subject being
immunized, such as human RSV being used to immunize humans. The
genome or antigenome of endogenous RSV can be modified, however, to
express RSV genes or gene segments from a combination of different
sources, e.g., a combination of genes or gene segments from
different RSV species, subgroups, or strains, or from an RSV and
another respiratory pathogen such as PIV.
In certain embodiments of the invention, chimeric RSV are provided
wherein genes or gene segments within a human RSV are replaced with
counterpart heterologous genes or gene segments from a non-human
RSV, e.g., a bovine or murine RSV. Alternatively, chimeric RSV may
incorporate genes or gene segments from a human RSV in a non-human
RSV recipient or background clone, e.g., a bovine or murine RSV
clone. Substitutions, deletions, and additions of RSV genes or gene
segments in this context can include part or all of one or more of
the NS1, NS2, N, P, M, SH, M2(ORF1), M2(ORF2) and L genes, or
non-immunogenic parts of the G and F genes. Also, human and
non-human RSV cis-acting sequences, such as promoter or
transcription signals, can be replaced with, respectively,
non-human or human counterpart sequences. Thus, methods are
provided to generate live attenuated bovine RSV by inserting human
attenuating genes or cis-acting sequences into a bovine RSV genome
or antigenome background.
Chimeric human/non-human RSV bearing heterologous genes or
cis-acting elements are selected for host range restriction and
other desired phenotypes favorable for vaccine use. In exemplary
embodiments, bovine RSV sequences are selected for introduction
into human RSV based on known aspects of bovine RSV structure and
function, as provided in, e.g., Pastey et al., J. Gen. Viol.
76:193-197 (1993); Pastey et al., Virus Res. 29:195-202 (1993);
Zamora et al., J. Gen. Virol. 73:737-741 (1992); Mallipeddi et al.,
J. Gen. Virol. 74:2001-2004 (1993); Mallipeddi et al., J. Gen.
Virol. 73:2441-2444 (1992); and Zamora et al., Virus Res.
24:115-121 (1992), each incorporated herein by reference, and in
accordance with the teachings disclosed herein.
In other embodiments of the invention, mutations of interest for
introduction within chimeric RSV are modeled after a tissue
culture-adapted nonpathogenic strain of pneumonia virus of mice
(the murine counterpart of human RSV) which lacks a cytoplasmic
tail of the G protein (Randhawa et al., Virology 207:240-245
(1995)). Accordingly, in one aspect of the invention the
cytoplasmic and/or transmembrane domains of one or more of the
human RSV glycoproteins, F, G and SH, are added, deleted, modified,
or substituted within a chimeric RSV using a heterologous
counterpart sequence (e.g., a sequence from a cytoplasmic, or
transmembrane domain of a F, G, or SH protein of murine pneumonia
virus) to achieve a desired attenuation. As another example, a
nucleotide sequence at or near the cleavage site of the F protein,
or the putative attachment domain of the G protein, can be modified
by point mutations, site-specific changes, or by alterations
involving entire genes or gene segments to achieve novel effects on
viral growth in tissue culture and/or infection and
pathogenesis.
Thus, infectious chimeric RSV intended for administration to humans
can be a human RSV that has been modified to contain genes from,
e.g., a bovine or murine RSV or a PIV, such as for the purpose of
attenuation. For example, by inserting a gene or gene segment from
PIV, a bivalent vaccine to both PIV and RSV can be provided.
Alternatively, a heterologous RSV species, subgroup or strain, or a
distinct respiratory pathogen such as PIV, may be modified, e.g.,
to contain genes that encode epitopes or proteins which elicit
protection against human RSV infection. For example, the human RSV
glycoprotein genes can be substituted for the bovine glycoprotein
genes such that the resulting chimeric RSV, which now bears the
human RSV surface glycoproteins in a bovine background, would
retain a restricted ability to replicate in a human host due to the
remaining bovine genetic background, while eliciting a protective
immune response in humans against human RSV strains.
In one embodiment of the invention, a chimeric bovine-human RSV
incorporates a substitution of the human RSV NP gene or gene
segment with a counterpart bovine NP gene or gene segment, which
chimera can optionally be constructed to incorporate additional
genetic changes, e.g., point mutations or gene deletions. For
example, replacement of a human RSV coding sequence (e.g., of NS1,
NS2, NP, etc.) or non-coding sequence (e.g., a promoter, gene-end,
gene-start, intergenic or other cis-acting element) with a
counterpart bovine or murine RSV sequence is expected to yield
chimeric RSV having a variety of possible attenuating and other
phenotypic effects. In particular, host range and other desired
effects are expected to arise from a non-human RSV gene imported
within a human RSV background, wherein the non-human gene does not
function efficiently in a human cell, e.g., from incompatibility of
the heterologous sequence or protein with a biologically
interactive human RSV sequence or protein (i.e., a sequence or
protein that ordinarily cooperates with the substituted sequence or
protein for viral transcription, translation, assembly, etc.)
In more detailed aspects of the invention, chimeric RSV are
employed as vectors for protective antigens of other pathogens,
particularly respiratory tract pathogens such as parainfluenza
virus (PIV). For example, chimeric RSV may be engineered which
incorporate sequences that encode protective antigens from PIV to
produce infectious, attenuated vaccine virus. The cloning of PIV
cDNA and other disclosure is provided in United States Patent
Application entitled PRODUCTION OF PARAINFLUENZA VIRUS VACCINES
FROM CLONED NUCLEOTIDE SEQUENCES, filed May 22, 1998, Ser. No.
09/083,793 (corresponding to International Publication No. WO
98/53078) and its priority, provisional application filed May 23,
1997, Ser. No. 60/047,575, each incorporated herein by reference.
This disclosure includes description of the following plasmids that
may be employed to produce infectious PIV viral clones: p3/7(131)
(ATCC 97990); p3/7(131)2G (ATCC 97889); and p218(131) (ATCC 97991);
each deposited under the terms of the Budapest Treaty with the
American Type Culture Collection (ATCC) of 10801 University
Boulevard, Manassas, Va. 20110-2209, U.S.A., and granted the above
identified accession numbers.
According to this aspect of the invention, a chimeric RSV is
provided which comprises a chimera of a RSV genomic or antigenomic
sequence and at least one PIV sequence, for example a
polynucleotide containing sequences from both RSV and PIV1, PIV2,
PIV3 or bovine PIV. For example, individual genes of RSV may be
replaced with counterpart genes from human PIV, such as the HN
and/or F glycoprotein genes of PIV1, PIV2, or PIV3. Alternatively,
a selected, heterologous gene segment, such as a cytoplasmic tail,
transmembrane domain or ectodomain of HN or F of HPIV1, HPIV2, or
HPIV3 can be substituted for a counterpart gene segment in, e.g.,
the same gene in an RSV clone, within a different gene in the RSV
clone, or into a non-coding sequence of the RSV genome or
antigenome. In one embodiment, a gene segment from HN or F of HPIV3
is substituted for a counterpart gene segment in RSV type A, to
yield constructs encoding chimeric proteins, e.g. fusion proteins
having a cytoplasmic tail and/or transmembrane domain of RSV fused
to an ectodomain of RSV to yield a novel attenuated virus, and/or a
multivalent vaccine immunogenic against both PIV and RSV.
In addition to the above described modifications to recombinant
RSV, different or additional modifications in RSV clones can be
made to facilitate manipulations, such as the insertion of unique
restriction sites in various intergenic regions (e.g., a unique
Stul site between the G and F genes) or elsewhere. Nontranslated
gene sequences can be removed to increase capacity for inserting
foreign sequences.
In another aspect of the invention, compositions (e.g., isolated
polynucleotides and vectors incorporating a chimeric RSV-encoding
cDNA) are provided for producing an isolated infectious chimeric
RSV. Using these compositions and methods, infectious chimeric RSV
are generated from a chimeric RSV genome or antigenome, a
nucleocapsid (N) protein, a nucleocapsid phosphoprotein (P), a
large (L) polymerase protein, and an RNA polymerase elongation
factor. In related aspects of the invention, compositions and
methods are provided for introducing the aforementioned structural
and phenotypic changes into a recombinant chimeric RSV to yield
infectious, attenuated vaccine viruses.
Introduction of the foregoing defined mutations into an infectious,
chimeric RSV clone can be achieved by a variety of well known
methods. By "infectious clone" is meant cDNA or its product,
synthetic or otherwise, which can be transcribed into genomic or
antigenomic RNA capable of serving as template to produce the
genome of an infectious virus or subviral particle. Thus, defined
mutations can be introduced by conventional techniques (e.g.,
site-directed mutagenesis) into a cDNA copy of the genome or
antigenome. The use of antigenome or genome cDNA subfragments to
assemble a complete antigenome or genome cDNA as described herein
has the advantage that each region can be manipulated separately
(smaller cDNAs are easier to manipulate than large ones) and then
readily assembled into a complete cDNA. Thus, the complete
antigenome or genome cDNA, or any subfragment thereof, can be used
as template for oligonucleotide-directed mutagenesis. This can be
through the intermediate of a single-stranded phagemid form, such
as using the Muta-gene.RTM. kit of Bio-Rad Laboratories (Richmond,
Calif.) or a method using a double-stranded plasmid directly as
template such as the Chameleon mutagenesis kit of Stratagene (La
Jolla, Calif.), or by the polymerase chain reaction employing
either an oligonucleotide primer or template which contains the
mutation(s) of interest. A mutated subfragment can then be
assembled into the complete antigenome or genome cDNA. A variety of
other mutagenesis techniques are known and available for use in
producing the mutations of interest in the RSV antigenome or genome
cDNA. Mutations can vary from single nucleotide changes to
replacement of large cDNA pieces containing one or more genes or
genome regions.
Thus, in one illustrative embodiment mutations are introduced by
using the Muta-gene phagemid in vitro mutagenesis kit available
from Bio-Rad. In brief, cDNA encoding a portion of an RSV genome or
antigenome is cloned into the plasmid pTZ18U, and used to transform
CJ236 cells (Life Technologies). Phagemid preparations are prepared
as recommended by the manufacturer. Oligonucleotides are designed
for mutagenesis by introduction of an altered nucleotide at the
desired position of the genome or antigenome. The plasmid
containing the genetically altered genome or antigenome fragment is
then amplified and the mutated piece is then reintroduced into the
full-length genome or antigenome clone.
The ability to introduce defined mutations into infectious RSV has
many applications, including the analyses of RSV molecular biology
and pathogenesis. For example, the functions of the RSV proteins,
including the NS1, NS2, SH, M2(ORF1) and M2(ORF2) proteins, can be
investigated and manipulated by introducing mutations which ablate
or reduce their level of expression, or which yield mutant protein.
In one exemplary embodiment hereinbelow, recombinant RSV is
constructed in which expression of a viral gene, namely the SH
gene, is ablated by deletion of the mRNA coding sequence and
flanking transcription signals. Surprisingly, not only could this
virus be recovered, but it grew efficiently in tissue culture. In
fact, its growth was substantially increased over that of the
wild-type, based on both yield of infectious virus and on plaque
size. This improved growth in tissue culture from the SH deletion
and other RSV derivatives of the invention provides useful tools
for developing RSV vaccines, which overcome the problem of RSV's
poor yield in tissue culture that had complicated production of
vaccine virus in other systems. These deletions are highly stable
against genetic reversion, rendering the RSV clones derived
therefrom particularly useful as vaccine agents.
The invention also provides methods for producing an infectious
chimeric RSV from one or more isolated polynucleotides, e.g., one
or more cDNAs. According to the present invention cDNA encoding a
RSV genome or antigenome is constructed for intracellular or in
vitro coexpression with the necessary viral proteins to form
infectious RSV. By "RSV antigenome" is meant an isolated
positive-sense polynucleotide molecule which serves as the template
for the synthesis of progeny RSV genome. Preferably a cDNA is
constructed which is a positive-sense version of the RSV genome,
corresponding to the replicative intermediate RNA, or antigenome,
so as to minimize the possibility of hybridizing with
positive-sense transcripts of the complementing sequences that
encode proteins necessary to generate a transcribing, replicating
nucleocapsid, i.e., sequences that encode N, P, L and M2(ORF1)
protein. In an RSV minigenome system, genome and antigenome were
equally active in rescue, whether complemented by RSV or by
plasmids, indicating that either genome or antigenome can be used
and thus the choice can be made on methodologic or other
grounds.
A native RSV genome typically comprises a negative-sense
polynucleotide molecule which, through complementary viral mRNAs,
encodes eleven species of viral proteins, i.e., the nonstructural
species NS1 and NS2, N, P, matrix (M), small hydrophobic (SH),
glycoprotein (G), fusion (F), M2(ORF1), M2(ORF2), and L,
substantially as described in Mink et al., Virology 185:615-624
(1991), Stec et al., Virology 183:273-287 (1991), and Connors et
al., Virol. 208:478-484 (1995), each incorporated herein by
reference. For purposes of the present invention the genome or
antigenome of the recombinant RSV of the invention need only
contain those genes or portions thereof necessary to render the
viral or subviral particles encoded thereby infectious. Further,
the genes or portions thereof may be provided by more than one
polynucleotide molecule, i.e., a gene may be provided by
complementation or the like from a separate nucleotide
molecule.
By recombinant RSV is meant a RSV or RSV-like viral or subviral
particle derived directly or indirectly from a recombinant
expression system or propagated from virus or subviral particles
produced therefrom. The recombinant expression system will employ a
recombinant expression vector which comprises an operably linked
transcriptional unit comprising an assembly of at least a genetic
element or elements having a regulatory role in RSV gene
expression, for example, a promoter, a structural or coding
sequence which is transcribed into RSV RNA, and appropriate
transcription initiation and termination sequences.
To produce infectious RSV from cDNA-expressed genome or antigenome,
the genome or antigenome is coexpressed with those RSV proteins
necessary to (i) produce a nucleocapsid capable of RNA replication,
and (ii) render progeny nucleocapsids competent for both RNA
replication and transcription. Transcription by the genome
nucleocapsid provides the other RSV proteins and initiates a
productive infection. Alternatively, additional RSV proteins needed
for a productive infection can be supplied by coexpression.
An RSV antigenome may be constructed for use in the present
invention by, e.g., assembling cloned cDNA segments, representing
in aggregate the complete antigenome, by polymerase chain reaction
(PCR; described in, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202,
and PCR Protocols: A Guide to Methods and Applications, Innis et
al., eds., Academic Press, San Diego (1990), incorporated herein by
reference) of reverse-transcribed copies of RSV mRNA or genome RNA.
For example, cDNAs containing the lefthand end of the antigenome,
spanning from an appropriate promoter (e.g., T7 RNA polymerase
promoter) and the leader region complement to the SH gene, are
assembled in an appropriate expression vector, such as a plasmid
(e.g., pBR322) or various available cosmid, phage, or DNA virus
vectors. The vector may be modified by mutagenesis and/or insertion
of synthetic polylinker containing unique restriction sites
designed to facilitate assembly. For example, a plasmid vector
described herein was derived from pBR322 by replacement of the
PstI-EcoR1 fragment with a synthetic DNA containing convenient
restriction enzyme sites. Use of pBR322 as a vector stabilized
nucleotides 3716-3732 of the RSV sequence, which otherwise
sustained nucleotide deletions or insertions, and propagation of
the plasmid was in bacterial strain DH10B to avoid an artifactual
duplication and insertion which otherwise occurred in the vicinity
of nt 4499. For ease of preparation the G, F and M2 genes can be
assembled in a separate vector, as can be the L and trailer
sequences. The righthand end (e.g., L and trailer sequences) of the
antigenome plasmid may contain additional sequences as desired,
such as a flanking ribozyme and tandem T7 transcriptional
terminators. The ribozyme can be hammerhead type (e.g., Grosfeld et
al., J. Virol. 69:5677-5686 (1995)), which would yield a 3' end
containing a single nonviral nucleotide, or can any of the other
suitable ribozymes such as that of hepatitis delta virus (Perrotta
et al., Nature 350:434-436 (1991)) which would yield a 3' end free
of non-RSV nucleotides. A middle segment (e.g., G-to-M2 piece) is
inserted into an appropriate restriction site of the leader-to-SH
plasmid, which in turn is the recipient for the
L-trailer-ribozyme-terminator piece, yielding a complete
antigenome. In an illustrative example described herein, the leader
end was constructed to abut the promoter for T7 RNA polymerase
which included three transcribed G residues for optimal activity;
transcription donates these three nonviral G's to the 5' end of the
antigenome. These three nonviral G residues can be omitted to yield
a 5' end free of nonviral nucleotides. To generate a nearly correct
3' end, the trailer end was constructed to be adjacent to a
hammerhead ribozyme, which upon cleavage would donate a single
3'-phosphorylated U residue to the 3' end of the encoded RNA.
In certain embodiments of the invention, complementing sequences
encoding proteins necessary to generate a transcribing, replicating
RSV nucleocapsid are provided by one or more helper viruses. Such
helper viruses can be wild-type or mutant. Preferably, the helper
virus can be distinguished phenotypically from the virus encoded by
the RSV cDNA. For example, it is desirable to provide monoclonal
antibodies which react immunologically with the helper virus but
not the virus encoded by the RSV cDNA. Such antibodies can be
neutralizing antibodies. In some embodiments, the antibodies can be
used in affinity chromatography to separate the helper virus from
the recombinant virus. To aid the procurement of such antibodies,
mutations can be introduced into the RSV cDNA to provide antigenic
diversity from the helper virus, such as in the HN or F
glycoprotein genes.
A variety of nucleotide insertions and deletions can be made in the
RSV genome or antigenome to generate an attenuated, chimeric clone.
The nucleotide length of the genome of wild-type human RSV (15,222
nucleotides) is a multiple of six, and members of the Paramyxovirus
and Morbillivirus genera typically abide by a "rule of six," i.e.,
genomes (or minigenomes) replicate efficiently only when their
nucleotide length is a multiple of six (thought to be a requirement
for precise spacing of nucleotide residues relative to
encapsidating NP protein). Alteration of RSV genome length by
single residue increments had no effect on the efficiency of
replication, and sequence analysis of several different minigenome
mutants following passage showed that the length differences were
maintained without compensatory changes. Thus, RSV lacks the strict
requirement of genome length being a multiple of six, and
nucleotide insertions and deletions can be made in the RSV genome
or antigenome without defeating replication of the recombinant RSV
of the present invention.
Alternative means to construct cDNA encoding an RSV genome or
antigenome include by reverse transcription-PCR using improved PCR
conditions (e.g., as described in Cheng et al., Proc. Natl. Acad.
Sci. USA 91:5695-5699 (1994); Samal et al., J. Virol 70:5075-5082
(1996), each incorporated herein by reference) to reduce the number
of subunit cDNA components to as few as one or two pieces. In other
embodiments different promoters can be used (e.g., T3, SP6) or
different ribozymes (e.g., that of hepatitis delta virus. Different
DNA vectors (e.g., cosmids) can be used for propagation to better
accommodate the large size genome or antigenome.
The N, P and L proteins, necessary for RNA replication, require an
RNA polymerase elongation factor such as the M2(ORF1) protein for
processive transcription. Thus M2(ORF1) or a substantially
equivalent transcription elongation factor for negative strand RNA
viruses is required for the production of infectious RSV and is a
necessary component of functional nucleocapsids during productive
infection.
The need for the M2(ORF1) protein is consistent with its role as a
transcription elongation factor. The need for expression of the RNA
polymerase elongation factor protein for negative strand RNA
viruses is a feature of the present invention. M2(ORF1) can be
supplied by expression of the complete M2-gene, either by the
chimeric genome or antigenome or by coexpression therewith,
although in this form the second ORF2 may also be expressed and
have an inhibitory effect on RNA replication. Therefore, for
production of infectious virus using the complete M2 gene the
activities of the two ORFs should be balanced to permit sufficient
expression of M(ORF1) to provide transcription elongation activity
yet not so much of M(ORF2) to inhibit RNA replication.
Alternatively, the ORF1 protein is provided from a cDNA engineered
to lack ORF2 or which encodes a defective ORF2. Efficiency of virus
production may also be improved by co-expression of additional
viral protein genes, such as those encoding envelope constituents
(i.e., SH, M, G, F proteins).
Isolated polynucleotides (e.g., cDNA) encoding the RSV genome or
antigenome and, separately or in cis, the N, P, L and M2(ORF1)
proteins, are inserted by transfection, electroporation, mechanical
insertion, transduction or the like, into cells which are capable
of supporting a productive RSV infection, e.g., HEp-2, FRhL-DBS2,
MRC, and Vero cells. Transfection of isolated polynucleotide
sequences may be introduced into cultured cells by, for example,
calcium phosphate-mediated transfection (Wigler et al., Cell 14:725
(1978); Corsaro and Pearson, Somatic Cell Genetics 7:603 (1981);
Graham and Van der Eb, Virology 52:456 (1973)), electroporation
(Neumann et al., EMBO J. 1:841-845 (1982)), DEAE-dextran mediated
transfection (Ausubel et al., (ed.) Current Protocols in Molecular
Biology, John Wiley and Sons, Inc., NY (1987), cationic
lipid-mediated transfection (Hawley-Nelson et al., Focus 15:73-79
(1993)) or a commercially available transfection regent, e.g.,
LipofectACE.RTM. (Life Technologies) (each of the foregoing
references are incorporated herein by reference).
The N, P, L and M2(ORF1) proteins are encoded by one or more
expression vectors which can be the same or separate from that
which encodes the genome or antigenome, and various combinations
thereof. Additional proteins may be included as desired, encoded by
its own vector or by a vector encoding a N, P, L, or M2(ORF1)
protein and/or the complete genome or antigenome. Expression of the
genome or antigenome and proteins from transfected plasmids can be
achieved, for example, by each cDNA being under the control of a
promoter for T7 RNA polymerase, which in turn is supplied by
infection, transfection or transduction with an expression system
for the T7 RNA polymerase, e.g., a vaccinia virus MVA strain
recombinant which expresses the T7 RNA polymerase (Wyatt et al.,
Virology, 210:202-205 (1995), incorporated herein by reference).
The viral proteins, and/or T7 RNA polymerase, can also be provided
from transformed mammalian cells, or by transfection of preformed
mRNA or protein.
Alternatively, synthesis of antigenome or genome can be conducted
in vitro (cell-free) in a combined transcription-translation
reaction, followed by transfection into cells. Or, antigenome or
genome RNA can be synthesized in vitro and transfected into cells
expressing RSV proteins.
To select candidate chimeric vaccine viruses according to the
invention, the criteria of viability, attenuation and
immunogenicity are determined according to well known methods.
Viruses which will be most desired in vaccines of the invention
must maintain viability, have a stable attenuation phenotype,
exhibit replication in an immunized host (albeit at lower levels),
and effectively elicit production of an immune response in a
vaccinee sufficient to confer protection against serious disease
caused by subsequent infection from wild-type virus. Clearly, the
heretofore known and reported RS virus mutants do not meet all of
these criteria. Indeed, contrary to expectations based on the
results reported for known attenuated RSV, viruses of the invention
are not only viable and more attenuated then previous mutants, but
are more stable genetically in vivo than those previously studied
mutants--retaining the ability to stimulate a protective immune
response and in some instances to expand the protection afforded by
multiple modifications, e.g., induce protection against different
viral strains or subgroups, or protection by a different
immunologic basis, e.g., secretory versus serum immunoglobulins,
cellular immunity, and the like. Prior to the invention, genetic
instability of the ts phenotype following replication in vivo has
been the rule for ts viruses (Murphy et al., Infect. Immun.
37:235-242 (1982)).
To propagate a RSV virus for vaccine use and other purposes, a
number of cell lines which allow for RSV growth may be used. RSV
grows in a variety of human and animal cells. Preferred cell lines
for propagating attenuated RS virus for vaccine use include
DBS-FRhL-2, MRC-5, and Vero cells. Highest virus yields are usually
achieved with epithelial cell lines such as Vero cells. Cells are
typically inoculated with virus at a multiplicity of infection
ranging from about 0.001 to 1.0 or more, and are cultivated under
conditions permissive for replication of the virus, e.g., at about
30-37.degree. C. and for about 3-5 days, or as long as necessary
for virus to reach an adequate titer. Virus is removed from cell
culture and separated from cellular components, typically by well
known clarification procedures, e.g., centrifugation, and may be
further purified as desired using procedures well known to those
skilled in the art.
Chimeric RSV which has been attenuated as described herein can be
tested in various well known and generally accepted in vitro and in
vivo models to confirm adequate attenuation, resistance to
phenotypic reversion, and immunogenicity for vaccine use. In in
vitro assays, the modified virus (e.g., a multiply attenuated,
biologically derived or recombinant RSV) is tested for temperature
sensitivity of virus replication, i.e. ts phenotype, and for the
small plaque phenotype. Modified viruses are further tested in
animal models of RSV infection. A variety of animal models have
been described and are summarized in Meignier et al., eds., Animal
Models of Respiratory Syncytial Virus Infection, Merieux Foundation
Publication, (1991), which is incorporated herein by reference. A
cotton rat model of RS infection is described in U.S. Pat. No.
4,800,078 and Prince et al., Virus Res. 3:193-206 (1985), which are
incorporated herein by reference, and is considered predictive of
attenuation and efficacy in humans and non-human primates. In
addition, a primate model of RSV infection using the chimpanzee is
predictive of attenuation and efficacy in humans, as is described
in detail in Richardson et al., J. Med. Virol. 3:91-100 (1978);
Wright et al., Infect. Immun. 37:397-400 (1982); Crowe et al.,
Vaccine 11:1395-1404 (1993), each incorporated herein by
reference.
The interrelatedness of data derived from rodents and chimpanzees
relating to the level of attenuation of RSV candidates can be
demonstrated by reference to FIG. 1, which is a graph correlating
the replication of a spectrum of respiratory syncytial subgroup A
viruses in the lungs of mice with their replication in chimpanzees.
The relative level of replication compared to that of wt RSV is
substantially identical, allowing the mouse to serve as a model in
which to initially characterize the level of attenuation of the
vaccine RSV candidate. The mouse and cotton rat models are
especially useful in those instances in which candidate RS viruses
display inadequate growth in chimpanzees. The RSV subgroup B
viruses are an example of the RS viruses which grow poorly in
chimpanzees.
Moreover, the therapeutic effect of RSV neutralizing antibodies in
infected cotton rats has been shown to be highly relevant to
subsequent experience with immunotherapy of monkeys and humans
infected with RSV. Indeed, the cotton rat appears to be a reliable
experimental surrogate for the response of infected monkeys,
chimpanzees and humans to immunotherapy with RSV neutralizing
antibodies. For example, the amount of RSV neutralizing antibodies
associated with a therapeutic effect in cotton rats as measured by
the level of such antibodies in the serum of treated animals (i.e.,
serum RSV neutralization titer of 1:302 to 1:518) is in the same
range as that demonstrated for monkeys (i.e., titer of 1:539) or
human infants or small children (i.e., 1:877). A therapeutic effect
in cotton rats was manifest by a one hundred fold or greater
reduction in virus titer in the lung (Prince et al., J. Virol.
61:1851-1854) while in monkeys a therapeutic effect was observed to
be a 50-fold reduction in pulmonary virus titer. (Hemming et al.,
J. Infect. Dis. 152:1083-1087 (1985)). Finally, a therapeutic
effect in infants and young children who were hospitalized for
serious RSV bronchiolitis or pneumonia was manifest by a
significant increase in oxygenation in the treated group and a
significant decrease in amount of RSV recoverable from the upper
respiratory tract of treated patients. (Hemming et al., Antimicrob.
Agents Chemother. 31:1882-1886 (1987)). Therefore, based on these
studies, the cotton rat constitutes a relevant model for predicting
success of chimeric RSV vaccines in infants and small children.
Other rodents, including mice, will also be similarly useful
because these animals are permissive for RSV replication and have a
core temperature more like that of humans (Wright et al., J.
Infect. Dis. 122:501-512 (1970) and Anderson et al., J. Gen. Virol.
71:(1990)).
In accordance with the foregoing description and based on the
Examples below, the invention also provides isolated, infectious
chimeric RSV compositions for vaccine use. The attenuated chimeric
virus which is a component of a vaccine is in an isolated and
typically purified form. By isolated is meant to refer to RSV which
is in other than a native environment of a wild-type virus, such as
the nasopharynx of an infected individual. More generally, isolated
is meant to include the attenuated virus as a component of a cell
culture or other artificial medium. For example, attenuated RSV of
the invention may be produced by an infected cell culture,
separated from the cell culture and added to a stabilizer which
contains other non-naturally occurring RS viruses, such as those
which are selected to be attenuated by means of resistance to
neutralizing monoclonal antibodies to the F-protein.
Chimeric RSV vaccines of the invention contain as an active
ingredient an immunogenically effective amount of RSV produced as
described herein. Biologically derived or recombinant RSV can be
used directly in vaccine formulations, or lyophilized. Lyophilized
virus will typically be maintained at about 4.degree. C. When ready
for use the lyophilized virus is reconstituted in a stabilizing
solution, e.g., saline or comprising SPG, Mg.sup.++ and HEPES, with
or without adjuvant, as further described below. The biologically
derived or recombinantly modified virus may be introduced into a
host with a physiologically acceptable carrier and/or adjuvant.
Useful carriers are well known in the art, and include, e.g.,
water, buffered water, 0.4% saline, 0.3% glycine, hyaluronic acid
and the like. The resulting aqueous solutions may be packaged for
use as is, or lyophilized, the lyophilized preparation being
combined with a sterile solution prior to administration, as
mentioned above. The compositions may contain pharmaceutically
acceptable auxiliary substances as required to approximate
physiological conditions, such as pH adjusting and buffering
agents, tonicity adjusting agents, wetting agents and the like, for
example, sodium acetate, sodium lactate, sodium chloride, potassium
chloride, calcium chloride, sorbitan monolaurate, triethanolamine
oleate, and the like. Acceptable adjuvants include incomplete
Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum,
which are materials well known in the art. Preferred adjuvants also
include Stimulon.TM. QS-21 (Aquila Biopharmaceuticals, Inc.,
Farmingham, Mass.), MPL.TM. (3-O-deacylated monophosphoryl lipid A;
RIBI ImmunoChem Research, Inc., Hamilton, Mont.), and
interleukin-12 (Genetics Institute, Cambridge, Mass.).
Upon immunization with a chimeric RSV vaccine composition as
described herein, via aerosol, droplet, oral, topical or other
route, the immune system of the host responds to the vaccine by
producing antibodies specific for one or more RSV virus proteins,
e.g., F and/or G glycoproteins. As a result of the vaccination the
host becomes at least partially or completely immune to RSV
infection, or resistant to developing moderate or severe RSV
disease, particularly of the lower respiratory tract.
Chimeric RSV vaccines of the invention may comprise attenuated
chimeric virus that elicits an immune response against a single RSV
strain or antigenic subgroup, e.g. A or B, or against multiple RSV
strains or subgroups. In this context, the chimeric RSV can elicit
a monospecific immune response or a polyspecific immune response
against multiple RSV strains or subgroups. Alternatively, chimeric
RSV having different immunogenic characteristics can be combined in
a vaccine mixture or administered separately in a coordinated
treatment protocol to elicit more effective protection against one
RSV strain, or against multiple RSV strains or subgroups.
The host to which the vaccine is administered can be any mammal
susceptible to infection by RSV or a closely related virus and
capable of generating a protective immune response to antigens of
the vaccinizing virus. Thus, suitable hosts include humans,
non-human primates, bovine, equine, swine, ovine, caprine,
lagamorph, rodents, etc. Accordingly, the invention provides
methods for creating vaccines for a variety of human and veterinary
uses.
The vaccine compositions containing the attenuated chimeric RSV of
the invention are administered to a patient susceptible to or
otherwise at risk of RS virus infection in an "immunogenically
effective dose" which is sufficient to induce or enhance the
individual's immune response capabilities against RSV. In the case
of human subjects, the attenuated virus of the invention is
administered according to well established human RSV vaccine
protocols, as described in, e.g., Wright et al., Infect Immun.
37:397-400 (1982), Kim et al., Pediatrics 52:56-63 (1973), and
Wright et al., J. Pediatr. 88:931-936 (1976), which are each
incorporated herein by reference. Briefly, adults or children are
inoculated intranasally via droplet with an immunogenically
effective dose of RSV vaccine, typically in a volume of 0.5 ml of a
physiologically acceptable diluent or carrier. This has the
advantage of simplicity and safety compared to parenteral
immunization with a non-replicating vaccine. It also provides
direct stimulation of local respiratory tract immunity, which plays
a major role in resistance to RSV. Further, this mode of
vaccination effectively bypasses the immunosuppressive effects of
RSV-specific maternally-derived serum antibodies, which typically
are found in the very young. Also, while the parenteral
administration of RSV antigens can sometimes be associated with
immunopathologic complications, this has never been observed with a
live virus.
In all subjects, the precise amount of chimeric RSV vaccine
administered and the timing and repetition of administration will
be determined based on the patient's state of health and weight,
the mode of administration, the nature of the formulation, etc.
Dosages will generally range from about 10.sup.3 to about 10.sup.6
plaque forming units (PFU) or more of virus per patient, more
commonly from about 10.sup.4 to 10.sup.5 PFU virus per patient. In
any event, the vaccine formulations should provide a quantity of
attenuated RSV of the invention sufficient to effectively stimulate
or induce an anti-RSV immune response, e.g., as can be determined
by complement fixation, plaque neutralization, and/or enzyme-linked
immunosorbent assay, among other methods. In this regard,
individuals are also monitored for signs and symptoms of upper
respiratory illness. As with administration to chimpanzees, the
attenuated virus of the vaccine grows in the nasopharynx of
vaccinees at levels approximately 10-fold or more lower than
wild-type virus, or approximately 10-fold or more lower when
compared to levels of incompletely attenuated RSV.
In neonates and infants, multiple administration may be required to
elicit sufficient levels of immunity. Administration should begin
within the first month of life, and at intervals throughout
childhood, such as at two months, six months, one year and two
years, as necessary to maintain sufficient levels of protection
against native (wild-type) RSV infection. Similarly, adults who are
particularly susceptible to repeated or serious RSV infection, such
as, for example, health care workers, day care workers, family
members of young children, the elderly, individuals with
compromised cardiopulmonary function, may require multiple
immunizations to establish and/or maintain protective immune
responses. Levels of induced immunity can be monitored by measuring
amounts of neutralizing secretory and serum antibodies, and dosages
adjusted or vaccinations repeated as necessary to maintain desired
levels of protection. Further, different vaccine viruses may be
indicated for administration to different recipient groups. For
example, an engineered chimeric RSV strain expressing a cytokine or
an additional protein rich in T cell epitopes may be particularly
advantageous for adults rather than for infants. RSV vaccines
produced in accordance with the present invention can be combined
with viruses expressing antigens of another subgroup or strain of
RSV to achieve protection against multiple RSV subgroups or
strains. Alternatively, the vaccine virus may incorporate
protective epitopes of multiple RSV strains or subgroups engineered
into one RSV clone as described herein.
Typically when different vaccine viruses are used they will be
administered in an admixture simultaneously, but they may also be
administered separately. For example, as the F glycoproteins of the
two RSV subgroups differ by only about 11% in amino acid sequence,
this similarity is the basis for a cross-protective immune response
as observed in animals immunized with RSV or F antigen and
challenged with a heterologous strain. Thus, immunization with one
strain may protect against different strains of the same or
different subgroup.
The chimeric RSV vaccines of the invention elicit production of an
immune response that is protective against serious lower
respiratory tract disease, such as pneumonia and bronchiolitis when
the individual is subsequently infected with wild-type RSV. While
the naturally circulating virus is still capable of causing
infection, particularly in the upper respiratory tract, there is a
very greatly reduced possibility of rhinitis as a result of the
vaccination and possible boosting of resistance by subsequent
infection by wild-type virus. Following vaccination, there are
detectable levels of host engendered serum and secretory antibodies
which are capable of neutralizing homologous (of the same subgroup)
wild-type virus in vitro and in vivo. In many instances the host
antibodies will also neutralize wild-type virus of a different,
nonvaccine subgroup.
Preferred chimeric RSV of the present invention exhibit a very
substantial diminution of virulence when compared to wild-type
virus that is circulating naturally in humans. The chimeric virus
is sufficiently attenuated so that symptoms of infection will not
occur in most immunized individuals. In some instances the
attenuated virus may still be capable of dissemination to
unvaccinated individuals. However, its virulence is sufficiently
abrogated such that severe lower respiratory tract infections in
the vaccinated or incidental host do not occur.
The level of attenuation of chimeric vaccine virus may be
determined by, for example, quantifying the amount of virus present
in the respiratory tract of an immunized host and comparing the
amount to that produced by wild-type RSV or other attenuated RSV
which have been evaluated as candidate vaccine strains. For
example, the attenuated chimeric virus of the invention will have a
greater degree of restriction of replication in the upper
respiratory tract of a highly susceptible host, such as a
chimpanzee, compared to the levels of replication of wild-type
virus, e.g., 10- to 1000-fold less. Also, the level of replication
of the attenuated RSV vaccine strain in the upper respiratory tract
of the chimpanzee should be less than that of the RSV A2 ts-1
mutant, which was demonstrated previously to be incompletely
attenuated in seronegative human infants. In order to further
reduce the development of rhinorrhea, which is associated with the
replication of virus in the upper respiratory tract, an ideal
vaccine candidate virus should exhibit a restricted level of
replication in both the upper and lower respiratory tract. However,
the attenuated viruses of the invention must be sufficiently
infectious and immunogenic in humans to confer protection in
vaccinated individuals. Methods for determining levels of RS virus
in the nasopharynx of an infected host are well known in the
literature. Specimens are obtained by aspiration or washing out of
nasopharyngeal secretions and virus quantified in tissue culture or
other by laboratory procedure. See, for example, Belshe et al., J.
Med. Virology 1:157-162 (1977), Friedewald et al., J. Amer. Med.
Assoc. 204:690-694 (1968); Gharpure et al., J. Virol. 3:414-421
(1969); and Wright et al., Arch. Ges. Virusforsch. 41:238-247
(1973), each incorporated herein by reference. The virus can
conveniently be measured in the nasopharynx of host animals, such
as chimpanzees.
In some instances it may be desirable to combine the chimeric RSV
vaccines of the invention with vaccines which induce protective
responses to other agents, particularly other childhood viruses.
For example, a chimeric RSV vaccine of the present invention can be
administered simultaneously with parainfluenza virus vaccine, such
as described in Clements et al., J. Clin. Microbiol. 29:1175-1182
(1991), which is incorporated herein by reference. In another
aspect of the invention the chimeric RSV can be employed as a
vector for protective antigens of other respiratory tract
pathogens, such as parainfluenza, by incorporating the sequences
encoding those protective antigens into the chimeric RSV genome or
antigenome which is used to produce infectious chimeric RSV, as
described herein.
In yet another aspect of the invention a chimeric RSV is employed
as a vector for transient gene therapy of the respiratory tract.
According to this embodiment the chimeric RSV genome or antigenome
incorporates a sequence which is capable of encoding a gene product
of interest. The gene product of interest is under control of the
same or a different promoter from that which controls RSV
expression. The infectious RSV produced by coexpressing the
recombinant RSV genome or antigenome with the N, P, L and M2(ORF1)
proteins and containing a sequence encoding the gene product of
interest is administered to a patient.
Administration is typically by aerosol, nebulizer, or other topical
application to the respiratory tract of the patient being treated.
Chimeric RSV is administered in an amount sufficient to result in
the expression of therapeutic or prophylactic levels of the desired
gene product. Examples of representative gene products which are
administered in this method include those which encode, for
example, those particularly suitable for transient expression,
e.g., interleukin-2, interleukin-4, gamma-interferon, GM-CSF,
G-CSF, erythropoietin, and other cytokines, glucocerebrosidase,
phenylalanine hydroxylase, cystic fibrosis transmembrane
conductance regulator (CFTR), hypoxanthine-guanine phosphoribosyl
transferase, cytotoxins, tumor suppressor genes, antisense RNAs,
and vaccine antigens.
The following examples are provided by way of illustration, not
limitation.
EXAMPLE I
Isolation and Characterization of Mutagenized Derivatives of
Cold-passaged RSV
This Example describes the chemical mutagenesis of incompletely
attenuated host range-restricted cpRSV to produce derivative ts and
sp mutations which are more highly attenuated and thus are
preferred for use in RSV vaccine preparations.
A parent stock of cold-passaged RSV (cpRSV) was prepared. Flow
Laboratories Lot 3131 virus, the cpRSV parent virus that is
incompletely attenuated in humans, was passaged twice in MRC-5
cells at 25.degree. C., terminally diluted twice in MRC-5 cells at
25.degree. C., then passaged three times in MRC-5 to create cpRSV
suspension for mutagenesis.
The cpRSV was mutagenized by growing the parent stock in MRC-5
cells at 32.degree. C. in the presence of 5-fluorouracil in the
medium at a concentration of 4.times.10.sup.-4M. This concentration
was demonstrated to be optimal in preliminary studies, as evidenced
by a 100-fold decrease in virus titer on day 5 of growth in cell
culture, compared to medium without 5-fluorouracil. The mutagenized
stock was then analyzed by plaque assay on Vero cells that were
maintained under an agar overlay, and after an appropriate interval
of incubation, plaques were stained with neutral red dye. 854
plaques were picked and the progeny of each plaque were separately
amplified by growth on fresh monolayers of Vero cells. The contents
of each of the tissue cultures inoculated with the progeny of a
single plaque of cpRSV-mutagenized virus were separately harvested
when cytopathic effects on the Vero cells appeared maximal. Progeny
virus that exhibited the temperature-sensitive (ts) or small-plaque
(sp) phenotype was sought by titering these plaque pools on HEp-2
cells at 32.degree. C. and 38.degree. C. Any virus exhibiting a sp
phenotype (plaque size that was reduced by 50% or more compared to
parental virus at 32.degree. C.) or a ts phenotype (100-fold or
greater reduction in titer at restrictive temperature [37.degree.
to 40.degree. C.] compared to 32.degree. C.) was evaluated further.
These strains were biologically cloned by serial
plaque-purification on Vero cells three times, then amplified on
Vero cells. The cloned strains were titered at 32.degree.,
37.degree., 38.degree., 39.degree. and 40.degree. C. (in an
efficiency of plaque formation (EOP) assay) to confirm their sp and
ts phenotypes. Because titers of some cloned strains were
relatively low even at the permissive temperature (32.degree.),
these viruses were passaged once in HEp-2 cells to create virus
suspensions for in vitro analysis. The phenotypes of the progeny of
the mutagenized cpRSV are presented on Table 1.
TABLE-US-00001 TABLE 1 The efficiency of plaque formation of nine
derivatives of cold-passaged RSV (cpts or cpsp mutants) in HEp-2
cells at permissive and restrictive temperatures The titer of virus
(log.sub.10pfu/ml) Shut-Off at the indicated temperature (.degree.
C.) temperature Small-plaques Virus 32 37 38 39 40 (.degree.
C.).sup.1 at 32 C. A2 wild-type 4.5 4.4 4.5 3.8 3.8 >40 no
cp-RSV 6.0 5.8 5.8 6.2 5.4 >40 no ts-1 5.7 4.5 2.7 2.4 1.7* 38
no cpsp143 4.2* 4.1* 3.8* 3.9* 3.8* >40 yes cpts368 6.7 6.3 6.1*
5.8** 2.0** 40 no cpts274 7.3 7.1 6.6 5.8* 1.0** 40 no cpts347 6.2
6.1 5.7* 5.5** <0.7 40 no cpts142 5.7 5.1 4.5* 3.7** <0.7 39
no cpts299 6.2 5.5 5.1* 2.0** <0.7 39 no cpts475 5.4 4.8* 4.2**
<0.7 <0.7 39 no cpts530 5.5 4.8* 4.5* <0.7 <0.7 39 no
cpts248 6.3 5.3** <0.7 <0.7 <0.7 38 no .sup.1Shut-off
temperature is defined as the lowest restrictive temperature at
which a 100-fold or greater reduction of plaque titer is observed
(bold figures in table). *Small-plaque phenotype (<50% wild-type
plaque size) **Pinpoint-plaque phenotype (<10% wild-type plaque
size)
One of the mutant progeny had the small plaque phenotype, RSV
cpsp143 (sp refers to the small plaque (sp) phenotype), and the
remaining mutant progeny had the ts phenotype. The RSV cpts mutants
exhibit a variation in ability to produce plaques in monolayer
cultures in vitro over the temperature range 37.degree. C. to
40.degree. C., with cpts368 retaining the ability to produce
plaques at 40.degree. C., whereas the most temperature-sensitive
(ts) virus, cpts248, failed to produce plaques at 38.degree. C.
Thus, several of the mutagenized cpRSV progeny exhibit a marked
difference from their cpRSV parent virus with respect to
temperature-sensitivity of plaque formation.
Replication and Genetic Stability Studies In Mice
The level of replication of the cpRSV derived mutants in the upper
and lower respiratory tracts of BALB/c mice was studied next (Table
2). It was found that cpts530 and cpts248, two of the mutants
exhibiting the greatest temperature sensitivity (see Table 1), were
about 7- to 12-fold restricted in replication in the nasal
turbinates of the mice (Table 2). However, none of the viruses was
restricted in replication in the lungs compared to the cpRSV parent
virus. This greater restriction of replication in the nasal
turbinates than in the lungs is not characteristic of ts mutants,
which generally are more restricted in replication in the warmer
lower respiratory tract (Richman and Murphy, Rev. Infect. Dis.
1:413-433 (1979). The virus produced in the lungs and nasal
turbinates retained the ts character of the input virus (data not
presented). The present findings suggested that the combination of
the ts mutations on the background of the mutations of the cp
parent virus has resulted in cpRSV ts progeny with a higher level
of stability of the ts phenotype after replication in vivo than had
been seen with previously studied ts mutants.
To further explore the level of genetic stability of the ts
phenotype of the cpRSV derived mutants, the efficiency of plaque
formation of virus present in the lungs and nasal turbinates of
nude mice was studied for two mutagenized cpRSV progeny that were
among the most ts, namely cpts248 and cpts530. Nude mice were
selected because they are immunocompromised due to congenital
absence of functional T-cells, and a virus can replicate for a much
longer period of time in these hosts. This longer period of
replication favors the emergence of virus mutants with altered
phenotype. The virus present on day 12 (NOTE: in normal mice, virus
is no longer detectable at this time) was characterized and found
to retain an unaltered ts phenotype (Table 3). As expected, the
ts-1 mutant included in the test as a positive control exhibited an
unstable ts phenotype in vivo. Thus, contrary to previous
evaluation of ts mutant viruses in rodents, the results show that a
high level of stability of the ts phenotype of the cpRSV derived
mutants following prolonged replication in rodents was achieved,
which represents a significant and heretofore unattained very
desirable property in the viruses of the invention.
TABLE-US-00002 TABLE 2 Replication of cpts and cpsp- RSV mutants in
BALB/c mice.sup.1 Virus titer at 32.degree. C. (mean log
.sub.10pfu/g tissue from the tissues of 8 animals .+-. standard
error) Animals Shutoff Day 4 Day 5 infected Temp. of Nasal Nasal
with virus (.degree. C.) Turbinates Lungs Turbinates Lungs 2 wild-
>40 5.0 .+-. 0.16 5.8 .+-. 0.20 5.0 .+-. 0.11 5.8 .+-. 0.19 type
cpRSV >40 4.7 .+-. 0.07 5.3 .+-. 0.18 4.8 .+-. 0.16 5.3 .+-.
0.21 ts-1 38 4.0 .+-. 0.19 4.7 .+-. 0.27 3.8 .+-. 0.33 4.9 .+-.
0.13 cpsp143 >40 4.5 .+-. 0.14 4.1 .+-. 0.37 4.4 .+-. 0.39 4.6
.+-. 0.39 cpts368 40 4.8 .+-. 0.15 5.1 .+-. 0.35 4.7 .+-. 0.08 5.4
.+-. 0.23 cpts274 40 4.2 .+-. 0.19 5.0 .+-. 0.15 4.2 .+-. 0.11 5.1
.+-. 0.55 cpts347 40 4.4 .+-. 0.32 4.9 .+-. 0.40 4.5 .+-. 0.33 5.2
.+-. 0.35 cpts142 39 4.1 .+-. 0.34 5.0 .+-. 0.19 4.3 .+-. 0.24 5.8
.+-. 0.40 cpts299 39 3.9 .+-. 0.11 5.2 .+-. 0.15 3.9 .+-. 0.32 5.0
.+-. 0.29 cpts475 39 4.0 .+-. 0.18 5.3 .+-. 0.25 4.1 .+-. 0.23 4.9
.+-. 0.42 cpts530 39 3.9 .+-. 0.18 5.3 .+-. 0.15 3.9 .+-. 0.14 5.3
.+-. 0.19 cpts248 38 3.9 .+-. 0.33 5.1 .+-. 0.29 4.2 .+-. 0.13 5.5
.+-. 0.35 .sup.1Mice were administered 10.sup.6.3 p.f.u.
intranasally in a 0.1 ml inoculum on day 0, then sacrificed on day
4 or 5.
TABLE-US-00003 TABLE 3 The genetic stability of RSV cpts-248 and
cpts-530 following prolonged replication in nude mice Efficiency of
plaque formation at indicated temperature of virus present in nasal
turbinates (n.t.) or lungs of nude mice sacrificed 12 days after
virus administration.sup.1 32.degree. C. 37.degree. C. Mean titer %
animals Mean titer Tissue (log.sub.10pfu with virus (log.sub.10pfu
Animals harvest or % animals per gram % animals with altered per
gram infected input virus Number of with virus tissue or ml with
virus ts tissue or ml with tested animals detectable
inoculum).sup.2 detectable phenotype inocul- um).sup.2 cpts-248
n.t. 19 100 3.8 .+-. 0.34 0 0 <2.0 '' lungs '' 90 2.0 .+-. 0.29
0 0 <1.7 cpts-530 n.t. 20 100 3.0 .+-. 0.26 0 0 <2.0 '' lungs
'' 100 2.4 .+-. 0.29 0 0 <1.7 ts-1 n.t. 19 100 3.7 .+-. 0.23 74
74 2.7 .+-. 0.57 '' lungs '' 100 2.5 .+-. 0.30 74 74 1.8 .+-. 0.21
Efficiency cpts-248 -- -- 4.9 -- <0.7 of plaque cpts-530 -- --
5.5 -- 3.7* formation ts-1 -- -- 6.1 -- 3.3 of input viruses
Efficiency of plaque formation at indicated temperature of virus
present in nasal turbinates (n.t.) or lungs of nude mice sacrificed
12 days after virus administration.sup.1 38.degree. C. 40.degree.
C. % animals Mean titer % animals Mean titer Tissue with virus
(log.sub.10pfu with virus (log.sub.10pfu Animals harvest or %
animals with altered per gram % animals with altered per gram
infected input virus with virus ts tissue or ml with virus ts
tissue or ml with tested detectable phenotype inoculum).sup.2
detectable phenotype inoc- ulum).sup.2 cpts-248 n.t. 0 0 <2.0 0
0 <2.0 '' lungs 0 0 <1.7 0 0 <1.7 cpts-530 n.t. 0 0
<2.0 0 0 <2.0 '' lungs 0 0 <1.7 0 0 <1.7 ts-1 n.t. 63
63 2.4 .+-. 0.36 10 10 2.0 .+-. 0.13 '' lungs 35 32 1.8 .+-. 0.15 0
0 <1.7 Efficiency cpts-248 -- <0.7 -- <0.7 of plaque
cpts-530 -- <0.7 -- <0.7 formation ts-1 -- 2.7 -- <0.7 of
input viruses .sup.1Plaque titers shown represent the mean
log.sub.10pfu/gram tissue of 19 or 20 samples .+-. standard error.
.sup.2Each animal received 10.sup.6.3 p.f.u. intranasally in a 0.1
ml inoculum of the indicated virus on day 0. *Small-plaque
phenotype only.
In Chimpanzees
The level of attenuation of the cpRSV ts derivative was next
evaluated in the seronegative chimpanzee, a host most closely
related to humans. Trials in chimpanzees or owl monkeys are
conducted according to the general protocol of Richardson et al.,
J. Med. Virol. 3:91-100 (1979); Crowe et al., Vaccine 11:1395-1404
(1993), which are incorporated herein by reference. One ml of
suspension containing approximately 10.sup.4 plaque-forming units
(PFU) of mutagenized, attenuated virus is given intranasally to
each animal. An alternate procedure is to inoculate the RSV into
both the upper and lower respiratory tract at a dose of 10.sup.4
PFU delivered to each site. Chimpanzees are sampled daily for 10
days, then every 3-4 days through day 20. The lower respiratory
tract of chimpanzees can be sampled by tracheal lavage according to
the protocol of Snyder et al., J. Infec. Dis. 154:370-371 (1986)
and Crowe et al., Vaccine 11:1395-1404 (1993). Some animals are
challenged 4 to 6 weeks later with the wild-type virus. Animals are
evaluated for signs of respiratory disease each day that
nasopharyngeal specimens are taken. Rhinorrhea is scored from 0 to
4+, with 2+ or greater being considered as evidence of significant
upper respiratory disease.
Virus is isolated from nasal and throat swab specimens and tracheal
lavage fluids by inoculation into RSV-sensitive HEp-2 cells as
described above. Quantities of virus can also be determined
directly by the plaque technique using HEp-2 cells as described in
Schnitzer et al., J. Virol. 17:431-438 (1976), which is
incorporated herein by reference. Specimens of serum are collected
before administration of virus and at 3 to 4 weeks post-inoculation
for determination of RSV neutralizing antibodies as described in
Mills et al., J. Immununol. 107:123-130 (1970), which is
incorporated herein by reference.
The most ts and attenuated of the cpRSV derivative (cpts248) was
studied and compared to wild-type RSV and the cpRSV parent virus
(Table 4). Replication of the cpRSV parent virus was slightly
reduced in the nasopharynx compared to wild-type, there was a
reduction in the amount of rhinorrhea compared to wild-type virus,
and there was an approximate 600-fold reduction in virus
replication in the lower respiratory tract compared to wild-type.
Clearly, the cp virus was significantly restricted in replication
in the lower respiratory tract of chimpanzees, a very desirable
property not previously identified from prior evaluations of cpRSV
in animals or humans. More significantly, the cpts 248 virus was
10-fold restricted in replication in the nasopharynx compared to
wild-type, and this restriction was associated with a marked
reduction of rhinorrhea. These findings indicated that the cpRSV
derived mutant possesses two highly desirable properties for a live
RSV vaccine, namely, evidence of attenuation in both the upper and
the lower respiratory tracts of highly susceptible seronegative
chimpanzees. The level of genetic stability of the virus present in
the respiratory tract of chimpanzees immunized with cpts248 was
evaluated next (Table 5). The virus present in the respiratory
tract secretions retained the ts phenotype, and this was seen even
with the virus from chimpanzee No. 3 on day 8 that was reduced
100-fold in titer at 40.degree. C. and exhibited the small plaque
phenotype at 40.degree. C., indicating that its replication was
still temperature-sensitive. This represents the most genetically
stable ts mutant identified prior to the time of this test. The
increased stability of the ts phenotype of the cpts248 and cpts530
viruses reflects an effect of the cp mutations on the genetic
stability of the mutations that contribute to the ts phenotype in
vivo. Thus, the ts mutations in the context of the mutations
already present in the cp3131 parent virus appear to be more stable
than would be expected in their absence. This important property
has not been previously observed or reported. Infection of
chimpanzees with the cpts 248 induced a high titer of serum
neutralizing antibodies, as well as antibodies to the F and G
glycoproteins (Table 6). Significantly, immunization with cpts248
protected the animals from wild-type RSV challenge (Table 7),
indicating that this mutant functions as an effective vaccine virus
in a host that is closely related to humans.
These above-presented findings indicate that the cpts248 virus has
many properties desirable for a live RSV vaccine, including: 1)
attenuation for the upper and lower respiratory tract; 2) increased
genetic stability after replication in vivo, even after prolonged
replication in immunosuppressed animals; 3) satisfactory
immunogenicity; and 4) significant protective efficacy against
challenge with wild-type RSV. The cpts530 virus shares with cpts248
similar temperature sensitivity of plaque formation, a similar
degree of restriction of replication in the nasal turbinates of
mice, and a high level of genetic stability in immunodeficient nude
mice, whereby it also represents an RS virus vaccine strain.
TABLE-US-00004 TABLE 4 Replication of cpts-RSV 248, cp-RSV, or
wild-type RSV A2 in the upper and lower respiratory tract of
seronegative chimpanzees Virus recovery Animal Infected Nasopharynx
Trachea with indicated Route of Chimpanzee Duration.sup.b Peak
titer Duration.sup.b Peak titer Rhinorrhea score virus inoculation
number (days) (log.sub.10pfu/ml) (days) (log.sub.10pfu/m- l)
Mean.sup.c Peak cpts-248 IN + IT 1 10 4.6 .sup. 8.sup.d 5.4 0.2 1
IN + IT 2 10 4.5 6 2.2 0.1 1 IN + IT 3 9 4.7 10 2.1 0.1 1 IN + IT 4
9 4.2 .sup. 8.sup.d 2.2 0.1 1 mean 9.5 mean 4.5 mean 8.0 mean 3.0
mean 0.1 cp-RSV IN 5 20 5.3 .sup. 8.sup.d 2.9 1.0 3 IN 6 16 5.8
.sup. 6.sup.d 3.0 1.8 3 IN + IT 7 13 4.3 .sup. 6.sup.d 3.0 0.6 1 IN
+ IT 8 16 5.0 .sup. 10.sup.d 2.8 0.5 1 mean 16 mean 5.1 mean 7.5
mean 2.9 mean 1.0 A2 wild-type IN 9 9 5.1 13 5.4 1.0 1 IN 10 9 6.0
8 6.0 1.7 4 IN + IT 11 13 5.3 8 5.9 2.1 3 IN + IT 12 9 5.4 8 5.6
1.0 3 mean 10 mean 5.5 mean 9.3 mean 5.7 mean 1.4 .sup.aIN =
Intranasal administration only, at a dose of 10.sup.4 p.f.u. in a
1.0 ml inoculum; IN + IT = Both intranasal and intratracheal
administration, 10.sup.4 p.f.u. in a 1.0 ml inoculum at each site.
.sup.bIndicates last day post-infection on which virus was
recovered. .sup.cMean rhinorrhea score represents the sum of daily
scores for a period of eight days surrounding the peak day of virus
shedding, divided by eight. Four is the highest score; zero is the
lowest score. .sup.dVirus isolated only on day indicated.
TABLE-US-00005 TABLE 5 Genetic stability of virus present in
original nasopharyngeal (NP) swabs or tracheal lavage (TL)
specimens obtained from animals experimentally infected with
cptsRSV 248. Virus Titer of RSV at indicated obtained on
temperature (log.sub.10pfu/ml) Chimpanzee NP swab or post-infection
Titer at Titer at Titer at number TL specimen day 32.degree. C.
39.degree. C. 40.degree. C. .sup. 1.sup.a NP 3 3.2 <0.7 NT '' 4
2.7 <0.7 NT '' 5 4.2 <0.7 NT '' 6 3.8 <0.7 NT '' 7 4.6
<0.7 NT '' 8 4.5 <0.7 NT '' 9 2.6 <0.7 NT '' 10 2.0
<0.7 NT TL 6 5.4 <0.7 NT '' 8 2.7 <0.7 NT .sup. 2.sup.a NP
3 3.2 <0.7 NT '' 4 3.7 <0.7 NT '' 5 4.5 <0.7 NT '' 6 4.1
<0.7 NT '' 7 3.3 <0.7 NT '' 8 4.2 <0.7 NT '' 9 2.8 <0.7
NT '' 10 1.6 <0.7 NT TL 6 2.2 <0.7 NT 3 NP 3 2.7 <0.7
<0.7 '' 4 3.4 <0.7 <0.7 '' 5 2.9 <0.7 <0.7 '' 6 3.3
<0.7 <0.7 '' 7 3.4 .sup. 0.7.sup.b <0.7 '' 8 4.7 .sup.
3.5.sup.b .sup. 2.0.sup.c '' 9 1.9 <0.7 <0.7 TL 6 1.8 <0.7
<0.7 '' 8 1.9 .sup. 1.2.sup.b <0.7 '' 10 2.1 .sup. 1.3.sup.b
<0.7 4 NP 3 3.2 <0.7 NT '' 4 2.7 <0.7 NT '' 5 3.4 <0.7
NT '' 6 3.3 <0.7 NT '' 7 4.2 <0.7 NT '' 8 3.5 <0.7 NT '' 9
2.1 <0.7 NT TL 8 2.2 <0.7 NT NT = Not tested .sup.aIsolates
(once-passaged virus suspensions with average titer log
.sub.10pfu/ml of 4.0) were generated from these chimpanzees from
each original virus-containing nasopharyngeal swab specimen or
tracheal lavage specimen and tested for efficiency of plaque
formation at 32.degree., 39.degree. and 40.degree. C. No isolate
was able to form plaques at 39.degree. C. Isolates from chimpanzees
3 and 4 were not tested in this manner. .sup.bThe percent titer at
39.degree. C. versus that at 32.degree. C.: NP swab day 7 = 0.2%,
NP swab day 8 = 6T, TL day 8 - 20%, TL day 10 = 16%. All plaques
were of small-plaque phenotype only; no wild-type size plaques
seen. .sup.cThe percent titer at 40.degree. C. versus that at
32.degree. C. was 0.2%. All plaques were of pinpoint-plaque
phenotype; wild-type size plaques were not detected.
TABLE-US-00006 TABLE 6 Serum antibody responses of chimpanzees
infected with RSV cpts-248, cp-RSV, or RSV A2 wild-type Serum
antibody titers (reciprocal mean log.sub.2) Animals No. of
Neutralizing ELISA-F ELISA-G immunized Chim- Day Day Day Day Day
Day with panzees 0 28 0 28 0 28 cpts-248 4 <3.3 10.7 7.3 15.3
6.3 9.8 cp-RSV 4 <3.3 11.2 11.3 15.3 9.3 12.3 RSVA2 4 <3.3
11.2 8.3 15.3 7.3 10.3 wild-type
TABLE-US-00007 TABLE 7 Immunization of chimpanzees with cpts-248
induces resistance to RSV A2 wild-type virus challenge on day 28
Response to challenge with 10.sup.4 p.f.u. wild-type virus
administered on day 28 Serum neutralizing antibody titer Virus
Recovery (reciprocal log.sub.2) on day Nasopharynx Trachea
indicated Virus used to Chimpanzee Duration Peak titer Duration
Peak titer Rhinorrhea score Day 42 or immunize animal number (days)
(log.sub.10pfu/ml) (days) (log.sub.10pfu/ml)- Mean* Peak Day 28 56
cpts-248 1 5 2.7 0 <0.7 0 0 10.1 11.0 2 9 1.8 0 <0.7 0 0 10.3
14.5 cp-RSV 5 5 1.0 0 <0.7 0 0 11.1 13.3 6 8 0.7 0 <0.7 0 0
11.4 12.9 none 9 9 5.1 13 5.4 1.0 1 <3.3 12.4 10 9 6.0 8 6.0 1.7
4 <3.3 13.2 11 13 5.3 8 5.9 2.1 3 <3.3 11.6 12 9 5.4 8 5.6
1.0 3 <3.3 11.2 *Mean rhinorrhea score represents the sum of
scores during the eight days of peak virus shedding divided by
eight. Four is the highest score. A score of zero indicates no
rhinorrhea detected on any day of the ten-day observation
period.
Further Attenuations
Since RS virus produces more symptoms of lower respiratory tract
disease in human infants than in the 1-2 year old chimpanzees used
in these experimental studies, and recognizing that mutants which
are satisfactorily attenuated for the chimpanzee may not be so for
seronegative infants and children, the cpts248 and 530 derivatives,
which possess the very uncharacteristic ts mutant properties of
restricted replication and attenuation in the upper respiratory
tract and a higher level of genetic stability, were further
mutagenized.
Progeny viruses that exhibited a greater degree of
temperature-sensitivity in vitro than cpts248 or that had the small
plaque phenotype were selected for further study. Mutant
derivatives of the cpts248 that possessed one or more additional ts
mutations were produced by 5-fluorouracil mutagenesis (Table 8). Ts
mutants that were more temperature-sensitive (ts) than the cpts248
parental strain were identified, and some of these had the small
plaque (sp) phenotype. These cpts248 derivatives were administered
to mice. cpts248/804, 248/955, 248/404, 248/26, 248/18, and 248/240
mutants were more restricted in replication in the upper and lower
respiratory tract of the mouse than their cpts248 parental virus
(Table 9). Thus, viable mutants of cpts248 which were more
attenuated than their cpts248 parental virus were identified, and
these derivatives of cpts248 exhibited a wide range of replicative
efficiency in mice, with cpts248/26 being the most restricted. The
ts phenotype of the virus present in nasal turbinates and lungs of
the mice was almost identical to that of the input virus,
indicating genetic stability. A highly attenuated derivative of
cpts248, the cpts248/404 virus, was 1000-fold more restricted in
replication in the nasopharynx compared to wild-type. The
cpts248/404 mutant, possessing at least three attenuating
mutations, was also highly restricted in replication in the upper
and lower respiratory tracts of four seronegative chimpanzees and
infection did not induce rhinorrhea (Table 10). Again, this virus
exhibited a high degree of reduction in replication compared to
wild-type, being 60,000-fold reduced in the nasopharynx and
100,000-fold in the lungs. Nonetheless, two chimpanzees which were
subsequently challenged with RSV wild-type virus were highly
resistant (Table 11).
Five small-plaque mutants of cpts248/404 were derived by chemical
mutagenesis in a similar fashion to that described above.
Suspensions of once-amplified plaque progeny were screened for the
small-plaque (sp) phenotype by plaque titration at 32.degree. C. on
HEp-2 cells, and working suspensions of virus were prepared as
described above.
Five of the plaque progeny of the mutagenized cpts248/404 virus
exhibited a stable sp phenotype. The shut-off temperature of each
mutant was 35.degree. C. or less (Table 12), suggesting that each
of these sp derivatives of the cpts248/404 virus also had acquired
an additional ts mutation. Following intranasal inoculation of
Balb/c mice with 10.sup.6.3 p.f.u. of a sp derivative of the
cpts248/404, virus could not be detected in the nasal turbinates of
mice inoculated with any of these sp derivatives. However, virus
was detected in low titer in the lungs in one instance. These
results indicate >300-fold restriction of replication in the
nasal turbinates and >10,000-fold restriction in lungs compared
with wild-type RSV.
Further ts derivatives of the cpts530 virus were also generated
(Table 13). As with the cpts248 derivatives, the cpts-530
derivatives were more restricted in replication in mice than the
cpts530 parental strain. One mutant, cpts-530/1009, was 30 times
more restricted in replication in the nasal turbinates of mice.
This cpts530 derivative, is also highly restricted in replication
in the upper and lower respiratory tract of seronegative
chimpanzees (Table 14). In the nasopharynx, cpts530 was 30-fold
restricted in replication, while cpts530/1009 was 100-fold
restricted compared to wild-type virus. Both of the cpts mutants
were highly restricted (20,000 to 32,000-fold) in the lower
respiratory tract compared with wild-type virus, even when the
mutants were inoculated directly into the trachea. Also,
chimpanzees previously infected with cpts530/1009, cpts530 or cpRSV
exhibited significant restriction of virus replication in the
nasopharynx and did not develop significant rhinorrhea following
subsequent combined intranasal and intratracheal challenge with
wild-type RSV (Table 15). In addition, chimpanzees previously
infected with any of the mutants exhibited complete resistance in
the lower respiratory tract to replication of wild-type challenge
virus.
These results were completely unexpected based on experience gained
during prior studies. For example, the results of an earlier study
indicated that the in vivo properties of RSV ts mutants derived
from a single cycle of 5-fluorouracil mutagenesis could not be
predicted a priori. Moreover, although one of the first four ts
mutants generated in this manner exhibited the same shut off
temperature for plaque formation as the other mutants, it was
overattenuated when tested in susceptible chimpanzees and
susceptible infants and young children (Wright et al., Infect
Immun. 37 (1):397-400 (1982). This indicated that the acquisition
of the ts phenotype resulting in a 37-38.degree. C. shut off
temperature for plaque formation did not reliably yield a mutant
with the desired level of attenuation for susceptible chimpanzees,
infants and children. Indeed, the results of studies with
heretofore known ts mutants completely fail to provide any basis
for concluding that introduction of three independent mutations (or
sets of mutations) into RSV by cold-passage followed by two
successive cycles of chemical mutagenesis could yield viable
mutants which retain infectivity for chimpanzees (and by
extrapolation, young infants) and exhibit the desired level of
attenuation, immunogenicity and protective efficacy required of a
live virus vaccine to be used for prevention of RSV disease.
The above-presented results clearly demonstrate that certain ts
derivatives of the cpRSV of the invention have a satisfactory level
of infectivity and exhibit a significant degree of attenuation for
mice and chimpanzees. These mutant derivatives are attenuated and
appear highly stable genetically after replication in vivo. These
mutants also induce significant resistance to RSV infection in
chimpanzees. Thus, these derivatives of cpRSV represent virus
strains suitable for use in a live RSV vaccine designed to prevent
serious human RSV disease.
TABLE-US-00008 TABLE 8 The efficiency of plaque formation of ten
mutants derived from RSV cpts248 by additional 5FU mutagenesis. The
titer of virus (log.sub.10pfu/ml) Shutoff at the indicated
temperature (.degree. C.) temperature Small- Virus 32 35 36 37 38
39 40 (.degree. C.).sup.1 at 32 C. plaques A2 wild-type 4.5 4.6 4.4
4.5 4.5 3.8 3.8 >40 no cpRSV 4.7 4.4 4.3 4.3 4.2 3.7 3.5 >40
no ts-1 5.6 5.4 4.9 4.4 2.7 2.0 <0.7 38 no cpts-248 3.4 3.0 2.6*
1.7** <0.7 <0.7 <0.7 38 no 248/1228 5.5* 5.3* 5.3**
<0.7 <0.7 <0.7 <0.7 37 yes 248/1075 5.3* 5.3* 5.1**
<0.7 <0.7 <0.7 <0.7 37 yes 248/965 4.5 4.2 4.2* <0.7
<0.7 <0.7 <0.7 37 no 248/967 4.4 3.7 3.6* <0.7 <0.7
<0.7 <0.7 37 no 248/804 4.9 4.5 4.0* <0.7 <0.7 <0.7
<0.7 37 no 248/955 4.8 3.7 2.8* <0.7 <0.7 <0.7 <0.7
36 no 248/404 3.6 2.9* <0.7 <0.7 <0.7 <0.7 <0.7 36
no 248/26 3.1 2.9* <0.7 <0.7 <0.7 <0.7 <0.7 36 no
248/18 4.0* 4.0** <0.7 <0.7 <0.7 <0.7 <0.7 36 yes
248/240 5.8* 5.7** <0.7 <0.7 <0.7 <0.7 <0.7 36 yes
.sup.1Shut-off temperature is defined as the lowest restrictive
temperature at which a 100-fold or greater reduction of plaque
titer in Hep-2 cells is observed (bold figures in table).
*Small-plaque phenotype (<50% wild-type plaque size).
**Pinpoint-plaque phenotype (<10% wild-type plaque size).
TABLE-US-00009 TABLE 9 Replication and genetic stability of ten
mutants derived from RSV cpts-248 in Balb/c mice.sup.1 Shutoff
temperature Virus titer [mean log.sub.10pfu/g tissue of six animals
.+-. standard error] Virus used to of Nasal turbinates Lungs infect
animal virus (.degree. C.) 32.degree. C. 36.degree. C. 37.degree.
C. 38.degree. C. 32.degree. C. 36.degree. C. 37.degree. C.
38.degree. C. A2 wild-type >40 5.1 .+-. 0.15 5.2 .+-. 0.23 5.2
.+-. 0.14 5.2 .+-. 0.27 6.1 .+-. 0.14 5.8 .+-. 0.23 6.0 .+-. 0.12
5.9 .+-. 0.17 cp-RSV >40 4.9 .+-. 0.20 5.1 .+-. 0.16 4.9 .+-.
0.24 4.9 .+-. 0.22 6.0 .+-. 0.16 5.9 .+-. 0.23 5.6 .+-. 0.15 5.6
.+-. 0.13 ts-1 38 3.9 .+-. 0.25 2.7 .+-. 0.27 2.4 .+-. 0.42 2.5
.+-. 0.29 4.1 .+-. 0.21 3.5 .+-. 0.23 2.6 .+-. 0.18 2.0 .+-. 0.23
cpts-248 38 4.0 .+-. 0.16 2.5 .+-. 0.34 <2.0 <2.0 4.4 .+-.
0.37 1.8 .+-. 0.15 <1.7 <1.7 248/1228 37 4.1 .+-. 0.15 2.4
.+-. 0.48 <2.0 <2.0 2.0 .+-. 0.37 <1.7 <1.7 <1.7
248/1075 37 4.2 .+-. 0.18 2.4 .+-. 0.40 <2.0 <2.0 5.5 .+-.
0.16 3.5 .+-. 0.18 <1.7 <1.7 248/965 37 3.8 .+-. 0.23 <2.0
<2.0 <2.0 4.5 .+-. 0.21 3.4 .+-. 0.16 <1.7 <1.7 248/967
37 4.4 .+-. 0.20 <2.0 <2.0 <2.0 5.4 .+-. 0.20 3.6 .+-.
0.19 <1.7 <1.7 248/804 37 2.9 .+-. 0.19 <2.0 <2.0
<2.0 3.6 .+-. 0.19 <1.7 <1.7 <1.7 248/955 36 3.2 .+-.
0.10 <2.0 <2.0 <2.0 3.2 .+-. 0.22 <1.7 <1.7 <1.7
248/404 36 .sup. 2.1 .+-. 0.31.sup.2 <2.0 <2.0 <2.0 .sup.
4.4 .+-. 0.12.sup.2 1.8 .+-. 0.20 <1.7 <1.7 248/26 36 <2.0
<2.0 <2.0 <2.0 2.3 .+-. 0.20 <1.7 <1.7 <1.7
248/18 36 2.9 .+-. 0.99 <2.0 <2.0 <2.0 4.3 .+-. 0.23 1.8
.+-. 0.15 <1.7 <1.7 248/240 36 2.9 .+-. 0.82 <2.0 <2.0
<2.0 3.9 .+-. 0.12 <1.7 <1.7 <1.7 .sup.1Mice were
administered 10.sup.6.3 p.f.u. intranasally under light anesthesia
on day 0, then sacrificed by CO.sub.2 asphyxiation on day 4.
.sup.2In a subsequent study, the level of replication of the
cpts-248/404 virus was found to be 2.4 .+-. 0.24 and 2.6 .+-. 0.31
in the nasal turbinates and lungs, respectively.
TABLE-US-00010 TABLE 10 Replication of cpts-RSV 248/404, cpts-RSV
248/18, cpts-RSV 248, cp-RSV, or wild-type RSV A2 in the upper and
lower respiratory tract of seronegative chimpanzees Virus recovery
Nasopharynx Trachea Animal infected with Route of Chimpanzee
Duration.sup.b Peak titer Duration.sup.b Peak titer Rhinorrhea
scores indicated virus inoculation number (days) (log.sub.10pfu/ml)
(days) (log.s- ub.10pfu/ml) Mean.sup.c Peak cpts-248/404 IN + IT 13
0 <0.7 0 <0.7 0 0 IN + IT 14 0 <0.7 0 <0.7 0 0 IN + IT
15 8 1.9 0 <0.7 0.3 2 IN + IT 16 9 2.0 0 <0.7 0.2 1 mean 4.3
mean 1.3 mean 0 mean <0.7 mean 0.1 mean 0.8 cpts-248# IN + IT 1
10 4.6 .sup. 8.sup.d 5.4 0.2 1 IN + IT 2 10 4.5 6 2.2 0.1 1 IN + IT
3 9 4.7 10 2.1 0.1 1 IN + IT 4 9 4.2 .sup. 8.sup.d 2.2 0.1 1 mean
9.5 mean 4.5 mean 8.0 mean 3.0 mean 0.1 mean 1.0 cp-RSV# IN 5 20
5.3 .sup. 8.sup.d 2.9 1.0 3 IN 6 16 5.8 .sup. 6.sup.d 3.0 1.8 3 IN
+ IT 7 13 4.3 .sup. 6.sup.d 3.0 0.6 1 IN + IT 8 16 5.0 .sup.
10.sup.d 2.8 0.5 1 mean 16 mean 5.1 mean 7.5 mean 2.9 mean 1.0 mean
2.0 A2 wild-type# IN 9 9 5.1 13 5.4 1.0 1 IN 10 9 6.0 8 6.0 1.7 4
IN + IT 11 13 5.3 8 5.9 2.1 3 IN + IT 12 9 5.4 8 5.6 1.0 3 mean 10
mean 5.5 mean 9.3 mean 5.7 mean 1.4 mean 2.8 .sup.aIN intranasal
administration only; IN + IT = Both intranasal and intratracheal
administration. .sup.bIndicates last day post-infection on which
virus was recovered. .sup.cMean rhinorrhea score represents the sum
of daily scores for a period of eight days surrounding the peak day
of virus shedding, divided by eight. Four is the highest score;
zero is the lowest score. .sup.dVirus isolated only on day
indicated. #These are the same animals included in Tables 4 and
7.
TABLE-US-00011 TABLE 11 Immunization of chimpanzees with
cpts-248/404 induces resistance to RSV A2 wild-type virus challenge
on day 28 Serum neutralizing antibody Virus Recovery titer
Nasopharynx Tracheal lavage [reciprocal log.sub.2] on day Virus
used to Chimpanzee Duration Peak titer Duration Peak titer
Rhinorrhea scores indicated.sup.b immunize animal number [days]
[log.sub.10pfu/ml] [days] [log.sub.10pfu/ml]- Mean.sup.a Peak Day
28 Day 49 or 56 cpts-248/404 13 0 <0.7 0 <0.7 0 0 7.9 9.0 14
8 3.4 0 <0.7 0 0 7.0 12.5 mean 4.0 mean 2.0 mean 0 mean <0.7
mean 0 mean 0 mean 7.5 mean 10.8 cpts-248# 1 5 2.7 0 <0.7 0 0
11.5 13.0 2 9 1.8 0 <0.7 0 0 12.7 14.5 mean 7.0 mean 2.3 mean 0
mean <0.7 mean 0 mean 0 mean 12.1 mean 13.8 cp-RSV# 5 5 1.0 0
<0.7 0 0 12.2 11.1 6 8 0.7 0 <0.7 0 0 11.9 9.9 mean 6.5 mean
0.9 mean 0 mean 0.7 mean 0 mean 0 mean 12.1 mean 10.5 None 9 9 5.1
13 5.4 1.0 1 <3.3 11.0 10 9 6.0 8 6.0 1.7 4 <3.3 9.8 11 13
5.3 8 5.9 2.1 3 <3.3 9.4 12 9 5.4 8 5.6 1.0 3 <3.3 14.5 mean
10 mean 5.5 mean 9.2 mean 5.7 mean 1.4 mean 2.8 mean <3.3 mean
11.2 .sup.aMean rhinorrhea score represents the sum of scores
during the eight days of peak virus shedding divided by eight. Four
is the highest score. A score of zero indicates no rhinorrhea
detected on any day of the ten-day observation period. #These are
the same animals included in Tables 4, 7 and 10. .sup.bSerum
neutralizing titers in this table, including those from animals
previously described, were determined simultaneously in one
assay.
TABLE-US-00012 TABLE 12 The efficiency of plaque formation and
replication of Balb/c mice of five small-plaque derivatives of RSV
cpts-248/404. Efficiency of plaque formation tested in HEp-2 cells
at permissive and restrictive temperatures The titer of virus
[log.sub.10pfu/ml] Shut-off Small- Replication in Balb/c mice.sup.2
at the indicated temperature [.degree. C.] temp plaques Nasal Virus
32 35 36 37 38 39 40 [.degree. C.].sup.1 at 32.degree. C.
turbinates.sup.3 Lungs.sup.3 A2 wild-type 6.0 6.1 6.0 5.8 5.9 5.4
5.4 >40 no 4.5 .+-. 0.34 5.6 .+-. 0.13 cp-RSV 6.2 6.2 6.0 6.0
5.9 5.6 5.4 >40 no 4.5 .+-. 0.10 5.3 .+-. 0.20 cpts-248 7.5 7.3
6.2** 5.3** <0.7 <0.7 <0.7 37 no 3.3 .+-. 0.35 4.8 .+-.
0.14 248/404 5.5 3.6** <0.7 <0.7 <0.7 <0.7 <0.7 36
no 2.4 .+-. 0.24 2.6 .+-. 0.31 248/404/774 2.9* <0.7 <0.7
<0.7 <0.7 <0.7 <0.7 .ltoreq.3- 5 yes <2.0 1.8 .+-.
0.24 248/404/832 5.5** <0.7 <0.7 <0.7 <0.7 <0.7
<0.7 .ltoreq.- 35 yes <2.0 <1.7 248/404/886 5.0** <0.7
<0.7 <0.7 <0.7 <0.7 <0.7 .ltoreq.- 35 yes <2.0
<1.7 248/404/893 5.4** <0.7 <0.7 <0.7 <0.7 <0.7
<0.7 .ltoreq.- 35 yes <2.0 <1.7 248/404/1030 4.4* 2.2**
<0.7 <0.7 <0.7 <0.7 <0.7 35 yes <- ;2.0
<1.7 .sup.1Shut-off temperature is defined as the lowest
restrictive temperature at which at 100-fold or greater reduction
of plaque titer is observed (bold figures in table). .sup.2Mice
were administered 10.sup.6.3 p.f.u. intranasally under light
anesthesia on day 0, then sacrificed by CO.sub.2 asphyxiation on
day 4 when tissues were harvested for virus titer. .sup.3Mean
log.sub.10pfu/g tissue of six animals .+-. standard error.
*Small-plaque phenotype (<50% wild-type plaque size).
**Pinpoint-plaque phenotype (<10% wild-type plaque size).
TABLE-US-00013 TABLE 13 The efficiency of plaque formation and
level of replication in mice of 14 mutants derived from RSV
cpts530, compared with controls In vitro efficiency of plaque
formation Replication in mice.sup.2 (mean log.sub.10pfu/g The titer
of virus (log.sub.10pfu/ml) at the indicated Shut-off tissue of six
animals .+-. SE) temperature (.degree. C.) Temp. Nasal RSV 32 34 35
36 37 38 39 40 (.degree. C.).sup.1 turbinates Lungs A2 6.3 6.3 6.1
6.2 6.3 6.3 6.1 5.6 >40 5.0 .+-. 0.14 5.8 .+-. 0.05 cpRSV 6.5
6.2 6.2 6.2 6.1 6.0 6.1 5.6 >40 n.d. n.d cpts248 6.3 6.3 6.3 6.3
3.7** <0.7 <0.7 <0.7 37/38 4.1 .+-. 0.08 5.1 .+-. 0.13
248/404 6.3 5.7* 4.3** <0.7 <0.7 <0.7 <0.7 <0.7
35/36 2.1 .+-. 0.19 3.6 .+-. 0.10 cpts530 6.2 6.3 6.2 6.1 6.2*
5.5** <0.7 <0.7 39 3.4 .+-. 0.09 4.3 .+-. 0.14 530/346 5.9
5.9 5.7 4.7 3.5 <0.7 <0.7 <0.7 37 3.3 .+-. 0.11 4.7 .+-.
0.09 530/977 5.0 4.4 3.6 3.4 2.8* <0.7 <0.7 <0.7 37 3.4
.+-. 0.11 2.7 .+-. 0.05 530/9 6.0 5.6 5.0 3.5* 3.5* <0.7 <0.7
<0.7 36 2.1 .+-. 0.06 3.5 .+-. 0.08 530/1009 4.8 4.0 3.7* 2.0**
1.5** <0.7 <0.7 <0.7 36 2.2 .+-. 0.15 3.5 .+-. 0.13
530/667 5.5 4.9 4.5* 2.0** 0.7 <0.7 <0.7 <0.7 36 2.4 .+-.
0.12 2.9 .+-. 0.15 530/1178 5.7 4.0 5.5 3.7** 2.0** <0.7 <0.7
<0.7 36 3.3 .+-. 0.06 42 .+-. 0.11 530/464 6.0 5.0* 4.7* 1.8**
<0.7 <0.7 <0.7 <0.7 36 <2.0 2.6 .+-. 0.10 530/403
5.7 5.1 4.3 2.9 <0.7 <0.7 <0.7 <0.7 36 <2.0 <1.7-
530/1074 5.1 4.6 4.1* <0.7 <0.7 <0.7 <0.7 <0.7 36
3.0 .+-. 0.13 3.8 .+-. 0.13 530/963 5.3 5.0 4.2* 0.7 <0.7
<0.7 <0.7 <0.7 36 2.0 .+-. 0.05 <1.7 530/653 5.4 5.1
4.5 <0.7 <0.7 <0.7 <0.7 <0.7 36 2.2 .+-. 0.10 3.1
.+-. 0.16 530/1003 5.6 4.1 2.5 2.1** <0.7 <0.7 <0.7
<0.7 35 <2.0 <- 1.7 530/1030 4.3 3.7* 1.7** <0.7
<0.7 <0.7 <0.7 <0.7 35 <2.0- 1.8 .+-. 0.13 530/188
5.0* 1.0* 1.0 <0.7 <0.7 <0.7 <0.7 <0.7 .gtoreq.34
&- lt;2.0 <1.7 n.d. = not done *Small-plaque phenotype
(<50% wild-type plaque size) **Pinpoint-plaque phenotype
(<10% wild-type plaque size) .sup.1Shut-off temperature is
defined as the lowest restrictive temperature at which a 100-fold
or greater reduction of plaque titer is observed (bold figures in
table). .sup.2Mice were administered 10.sup.6.3 p.f.u. intranasally
under light anesthesia on day 0, then sacrificed by CO.sub.2
asphyxiation on day 4.
TABLE-US-00014 TABLE 14 Replication of cpts-530/1009, cp-RSV, or
wild-type RSV A2 in the upper and lower respiratory tract of
seronegative chimpanzees induces serum neutralizing antibodies. Day
28 Animals Virus Replication reciprocal infected with Nasopharynx
Trachea Rhinorrhea serum 10.sup.4 pfu of Route of Chimpanzee
Duration.sup.b Peak Titer Duration.sup.b Peak Titer Scores
neutralizing indicated virus inoculation Number [days]
[log.sub.10pfu/ml] [days] [log.s- ub.10pfu/ml] Mean.sup.c Peak
antibody titer.sup.g cpts-530/1009 IN + IT 1 9 3.1 0 <1.0 0.5 2
1,097 IN + IT 2 10 4.0 .sup. 10.sup.a 1.8 0.5 2 416 IN + IT 3 9 4.0
0 <1.0 0.8 2 1,552 IN + IT 4 9 3.3 0 <1.0 0.4 1 1,176 mean
9.3 mean 3.6 mean 2.5 mean 1.2 mean 0.5 mean 1.3 mean 1,060
cpts-530 IN + IT 5 9 3.5 .sup. 4.sup.c 2.6 0.3 1 10,085 IN + IT 6 9
5.2 0 <1.0 1.1 3 3,566 IN + IT 7 8 3.3 0 <1.0 0.6 2 588 IN +
IT 8 8 4.4 0 <1.0 0.5 2 1,911 mean 8.5 mean 4.1 mean 1.0 mean
1.4 mean 0.6 mean 2.0 mean 4,038 cp-RSV IN .sup. 9.sup.d 20 5.3
.sup. 8.sup.e 2.9 1.0 3 416 IN .sup. 10.sup.d 16 5.8 .sup. 6.sup.e
3.0 1.8 3 2,048 IN + IT .sup. 11.sup.d 13 4.3 .sup. 6.sup.e 3.0 0.6
1 776 IN + IT .sup. 12.sup.d 16 5.0 .sup. 10.sup.e 2.8 0.5 1 891
mean 16 mean 5.1 mean 7.5 mean 2.9 mean 1.0 mean 2.0 mean 1,033 A2
wild-type IN .sup. 13.sup.f 9 5.1 13 5.4 1.0 1 1,351 IN .sup.
14.sup.f 9 6.0 8 6.0 1.7 4 676 IN + IT .sup. 15.sup.d 13 5.3 8 5.9
2.1 3 1,261 IN + IT .sup. 16.sup.d 9 5.4 8 5.6 1.0 3 20,171 mean 10
mean 5.5 mean 9.3 mean 5.7 mean 1.4 mean 2.8 mean 5,865 .sup.aIN =
Intranasal only; IN + IT = Both intranasal and intratracheal
administration. .sup.bIndicates last day post-infection on which
virus was recovered. .sup.cMean rhinorrhea score represents the sum
of daily scores for a period of eight days surrounding the peak day
of virus shedding, divided by eight. Four is the highest score;
zero is the lowest score. .sup.dAnimals from Crowe, et al. Vaccine
12: 691-699 [1994]. .sup.eVirus isolated only on day indicated.
.sup.fAnimals from Collins, et al. Vaccine 8: 164-168 [1990].
.sup.gDetermined by complement-enhanced 60% plaque reduction of RSV
A2 in HEp-2 cell monolayer cultures. All titers were determined
simultaneously in a single assay. The reciprocal titer of each
animal on day 0 was < 10.
TABLE-US-00015 TABLE 15 Immunization of chimpanzees with
cpts-530/1009 or cpts-530 induces resistance to wild-type RSV A2
virus challenge on day 28 Virus replication Serum neutralizing
antibody Nasopharynx Tracheal lavage Rhinorrhea [reciprocal
log.sub.2] on day Virus used for Chimpanzee Duration Peak titer
Duration Peak titer scores indicated.sup.d immunization number
[days] [log.sub.10pfu/ml] [days] [log.sub.10pfu/ml] Me- an.sup.a
Peak Day 28 Day 49 or 56 cpts-530/1009 3 7 2.1 0 <0.7 0 0 1,552
3,823 4 0 <0.7 0 <0.7 0 0 1,176 1,911 cpts-530 5 0 <0.7 0
<0.7 0 0 10,085 6,654 6 0 <0.7 0 <0.7 0.3 2 3,566 1,911
cp-RSV .sup. 11.sup.b 5 1.0 0 <0.7 0 0 776 2,048 .sup. 12.sup.b
8 0.7 0 <0.7 0 0 891 1,783 None .sup. 13.sup.b 9 5.1 13 5.4 1.0
1 <10 1,351 .sup. 14.sup.b 9 6.0 8 6.0 1.7 4 <10 676 .sup.
15.sup.c 13 5.3 8 5.9 2.1 3 <10 1,261 .sup. 16.sup.c 9 5.4 8 5.6
1.0 3 <10 20,171 .sup.aMean rhinorrhea scores represent the sum
of scores during the eight days of peak virus shedding divided by
eight. Four is the highest score. .sup.bAnimals from Crowe et al.
Vaccine 12:691-699 [1994]. .sup.cAnimals from Collins et al.
Vaccine 8:164-168 [1990]. .sup.dSerum neutralizing titers in this
table, including those from animals previously described, were
determined simultaneously in one assay.
Effect of Passively-Acquired Serum RSV Antibodies on cpts Mutants
in Chimpanzees
In order to examine the effect of passively-acquired serum RSV
antibodies on attenuation, immunogenicity and protective efficacy
of various cpts mutants of the invention in chimpanzees, the in
vivo replication of cpts248, cpts248/404, and cpts530/1009, was
evaluated in seronegative chimpanzees which were infused with RSV
immune globulin two days prior to immunization (Table 16). Antibody
was passively transferred in order to simulate the conditions which
obtain in young infants who possess maternally-derived RSV
antibodies. In this way, it was possible to assess the
immunogenicity of each indicated mutant in the presence of passive
RSV antibodies to determine whether the replication of highly
attenuated viruses might be so reduced in infants with a moderate
to high titer of passive antibodies as to preclude the induction of
a protective immune response. It would also be possible to define
the nature of the antibody response to immunization in the presence
of passively acquired antibodies, and to define the extent and
functional activity of the antibody response to virus challenge.
The level of virus replication in the nasopharynx and the
associated clinical score for the attenuated mutants was either not
altered or only moderately altered by the presence of serum RSV
antibodies when the infection of those animals was compared to that
of non-infused seronegative chimpanzees. In contrast, the presence
of passively-acquired antibodies effectively prevented virus
replication of cpts248 in the lower respiratory tract. Because the
other two mutants were already highly restricted in the lungs, the
similar effect of passive antibodies could not be evaluated against
those mutants.
Infusion of human RSV immune globulin yielded moderately high serum
levels of RSV F antibodies (titer 1:640 to 1:1600), and
neutralizing antibodies (titer 1:199 to 1:252), but not appreciable
amounts of serum RSV G antibody detectable above background (Table
17). Chimpanzees who were infused with human RSV antibodies prior
to immunization with cpts248/404, cpts530/1009, or cpts248
developed only one-tenth the quantity of RSV F antibodies and about
one-half the titer of neutralizing antibodies by day 42
post-immunization, compared to non-infused immunized animals tested
28 days post-immunization. Because the infused human IgG contained
substantial amounts of RSV F and RSV neutralizing antibodies, the
residual antibodies from the infusion present in the 42-day serum
samples could not be distinguished from antibodies produced de novo
in response to immunization. Given the half-life of human serum IgG
antibodies in chimpanzees (Prince et al., Proc. Natl. Acad. Sci.
USA 85:6944-6948), the observed levels of F and neutralizing
antibodies on day 42 following immunization with cpts are higher
than would be predicted for a residuum of the infusion. In
addition, the RSV G antibody response following immunization of the
infused animals confirms that these chimpanzees mounted an immune
response to immunization.
Four to six weeks following immunization the chimpanzees were
challenged with wild-type RSV. Each of the animals exhibited
complete resistance in their lower respiratory tract, whether or
not human IgG was infused two days before immunization (Table 18).
Non-infused animals developed a modest neutralizing antibody
response to challenge or none at all (Table 17). In contrast, the
infused chimpanzees uniformly developed an unusually high titer of
RSV neutralizing antibodies in response to wild-type virus
challenge despite the fact that virus replication had been severely
restricted (Tables 17 and 18). Moreover, following immunization in
the presence of antibodies the most attenuated virus, cpts248/404,
which exhibited the lowest level of virus replication and
immunization, had the highest post-challenge neutralizing antibody
titers (Table 17). In contrast, the least attenuated virus,
cpts248, had the lowest post-challenge neutralizing antibody titer
of the three groups of infused animals. In addition to an increase
in the quantity of the antibodies induced by immunization in the
presence of antibodies, the quality of the antibodies, as measured
by the neutralizing to ELISA F antibody titer ratio, was
significantly greater than that induced by immunization in
seronegative animals (Table 17). The neutralizing/ELISA F ratio of
the antibodies produced in the infused immunized animals
post-challenge was about 10- to 20-fold higher than in the
non-infused animals and was consistent in all groups, regardless of
mutant used to immunize (Table 17).
The presence of passively-acquired antibodies at the time of
immunization with a live virus vaccine might alter the immune
response to vaccine in three distinct ways. First, a significant
decrease in the level of replication of vaccine virus might occur
that results in decreased immunogenicity. It is possible that the
passively-transferred RSV antibodies could restrict the replication
of the vaccine viruses, especially the most defective mutants, and
greatly decrease their immunogenicity. The results presented herein
indicate that replication of the least attenuated mutant (cpts248)
in the lower respiratory tract was indeed abrogated by the presence
of passively-acquired serum IgG RSV antibodies, whereas replication
in the upper respiratory tract did not appear to be significantly
affected. The replication of the least attenuated mutant tested,
cpts248, was .gtoreq.200-fold more (i.e. completely) restricted in
the lower respiratory tract in the presence of antibodies. The
level of replication of the more attenuated mutants, cpts530/1009
and cpts248/404, in the lower respiratory tract was highly
restricted even in the seronegative animals. Therefore, a
significant effect of passive antibodies on virus replication could
not be detected. Immunization with each of the three attenuated
mutants induced a high degree of protection against wild-type
challenge in both the upper and lower respiratory tracts, whether
or not passively-acquired RSV antibodies were present at the time
of immunization. Thus, the level of replication of the vaccine
viruses in the upper respiratory tract of passively-immunized
chimpanzees was sufficient to induce a high level of resistance to
wild-virus challenge which was comparable to that induced in
non-infused animals.
Second, passive antibodies can alter the immune response to
infection by causing a decrease in the amount and functional
activity of antibodies that are induced. For this reason the
magnitude and the character of the antibody response to live virus
immunization in the presence of passive antibodies was analyzed.
Postimmunization serum ELISA IgG F antibody titers of immunized,
infused animals were 10-fold lower than the postimmunization F
titers of non-infused seronegative animals. The serum RSV
neutralizing antibody response was also slightly decreased in those
animals, on average being 2-fold lower than in non-infused animals.
Because some of the ELISA F and neutralizing antibodies detected
postimmunization represent residual antibodies from the infusion,
the actual decrease of the neutralizing and F antibody response
caused by preexisting antibodies is probably even more significant
than is apparent. Moreover, the human immune globulin preparation
used contained a low level of antibodies to the G glycoprotein of
RSV (Table 17). This petted an examination of the IgG RSV G
glycoprotein antibody response of the chimpanzees to infection with
the candidate vaccine viruses. The G antibody responses
demonstrated at least a 4-fold or greater increase, indicating that
each of the passively-immunized animals was infected by vaccine
virus, including chimpanzees immunized with cpts248/404 which did
not shed virus. The magnitude of the G antibody response to
immunization did not appear to be adversely influenced by the
passively transferred antibodies.
Thirdly, the antibody response to RSV wild-type virus challenge of
animals immunized in the presence of passively-acquired antibodies
could be altered. Chimpanzees immunized in the absence of infused
antibodies exhibited significant resistance to subsequent RSV
challenge. In addition, these animals failed to develop an
appreciable antibody response to challenge virus. Although each of
the 6 infused, immunized animals also exhibited significant
resistance to RSV, a greatly enhanced antibody response to
challenge was observed. Post-challenge F or G antibody levels in
the treated animals immunized with cpts530/1009 or cpts248/404 were
increased at least 10-fold, while the neutralizing antibody
response represented as much as an 800-fold increase. These results
suggest that repeated immunization of infants possessing maternal
antibodies with live attenuated mutants beginning very early in
life might stimulate effective resistance and an associated
enhanced secondary antibody response of high quality. The mechanism
responsible for an enhanced immune response to second infection in
the absence of appreciable replication of the challenge virus is
not understood. The presence of serum antibodies at the time of
immunization, while allowing a modest antibody response to
immunization in infused animals, favors the development of a B cell
repertoire that elaborates antibodies of highly functional activity
following subsequent RSV challenge.
The results reported herein are highly significant in that for the
first time live attenuated RSV virus vaccine has been shown to be
efficacious in an animal model which mimics the target population
for an RSV vaccine, i.e. the four to six week old infant having
passively acquired RSV neutralizing antibodies as a result of
transplacental transfer from the mother. The importance of this
finding is clear from the fact that, as discussed, supra, the high
expectation that the passively transferred RSV antibodies would
have inhibited the replication of the cpts vaccine, rendering it
non-immunogenic and non-protective has, surprisingly, not been
borne out.
TABLE-US-00016 TABLE 16 Replication of RSV cpts-248/404, cpts-248,
or cpts-530/1009 in the upper and lower respiratory tract of
seronegative chimpanzees, some of which were infused with RSV
neutralizing antibodies two days prior to immunization. Virus
Replication Reciprocal serum Trachea Animal infected RSV
neutralizing Nasopharynx Peak Rhinorrhea within 10.sup.4 pfu of
antibody titer at time Chimpanzee Duration Peak Titer Duration
Titer Scores indicated virus of immunization Number [days]
[log.sub.10pfu/ml] [days] [log.sub.10pfu/ml] P- eak Mean
cpts-248/404 <10 17 0 <0.7 0 <0.7 0 0 <10 20 9 <0.7
0 <0.7 0 0 <10 19 8 1.9 0 <0.7 2 0.3 <10 20 9 2.0 0
<0.7 1 0.2 [mean 4.3] [mean 1.3] [mean 0] [mean <0.7] [mean
0.8] [mean 0.1] 142 21 0 <0.7 0 <0.7 2 0.6 156 22 0 <0.7 0
<0.7 1 0.1 [mean 0] [mean <0.7] [mean 0] [mean <0.7] [mean
1.5] [mean 0.4] cpts-530/1009 <10 1 9 3.1 0 <1.0 1 0.3 <10
2 10 4.0 10 1.8 1 1.1 <10 3 9 4.0 0 <1.0 1 0.6 <10 4 9 3.3
0 <1.0 1 0.5 [mean 9.3] [mean 3.6] [mean 2.5] [mean 1.2] [mean
1.0] [mean 0.6] 259 23 8 3.0 0 <0.7 1 0.1 190 24 7 1.2 0 <0.7
1 0.2 [mean 7.5] [mean 2.1] [mean 0] [mean <0.7] [mean 1.0]
[mean 0.2] cpts-248 <10 25 10 4.6 8 5.4 1 0.2 <10 26 10 4.5 6
2.2 1 0.1 <10 27 9 4.7 10 2.1 1 0.1 <10 28 9 4.2 8 2.2 1 0.1
[mean 9.5] [mean 4.5] [mean 8.0] [mean 3.0] [mean 1.0] [mean 0.1]
290 29 13 4.2 0 <0.7 2 0.4 213 30 16 4.7 0 <0.7 3 0.9 [mean
14.5] [mean 4.5] [mean 0] [mean <0.7] [mean 2.5] [mean 0.7]
TABLE-US-00017 TABLE 17 Serum antibody response of chimpanzees
immunized on day 0 with RSV cpts-248/404, cpts-248, or
cpts-530/1009, in the presence or absence of passively-transferred
antibodies, and challenged 4 to 6 weeks later with wild-type RSV
A2. RSV F RSV G Neutralizing.sup.3 Animals Day 0 Day 0 Day 0
infect- In- (48 hrs. (48 hrs. (48 hrs. ed fused after Post 28 after
Post 28 after Post 28 with No. with infusion im- days infusion im-
days infusion im- days indi- of anti- Prior of muni- post- Prior of
muni- post- Prior of muni- po- st cated ani- bo- to anti- za- chal-
to anti- za- chal- to anti- za- chal- virus mals dies study bodies)
tion.sup.1 lenge.sup.2 study bodies) tion.su- p.1 lenge.sup.2 study
bodies) tion.sup.1 lenge.sup.2 F G cpts- 4 no <40 <40 6,400
2,560 60 60 1,000 1,600 <10 <10 208 3- 62 0.2 0.1 248/ 404 2
yes <40 1,600 640 25,600 100 100 1,600 21,760 <10 199 111
92,681 - 4.3 3.6 cpts- 4 no <40 <40 6,400 10,240 <40
<40 10,240 2,560 <10 &l- t;10 256 2,521 1.0 0.3 530/ 1009
2 yes <40 1,600 640 10,240 40 100 400 10,240 <10 225 52
37,641 3.7 - 3.7 cpts- 4 no <40 <40 7,840 6,400 <40 <40
250 2,560 <10 <10- 147 338 0.1 0.1 248 2 yes <40 640 1,600
5,400 40 40 1,600 5,440 <10 252 119 26,616 4.9 - 4.9 .sup.1The
day on which postimmunization titer was determined was also the day
on which challenge was performed, i.e., day 28 for animals not
infused with antibody, day 42 for animals infused. .sup.2Values
determined from samples taken 28 days after challenge. Challenge
performed on day 28 postimmunization for animals not infused with
antibody, day 42 for animals infused. .sup.3Determined by
complement-enhanced 60% plaque reduction of RSV A2 in HEp-2 cell
monolayer cultures. Neutralizing antibody titer represents the mean
value from two tests.
TABLE-US-00018 TABLE 18 Immunization of chimpanzees with RSV
cpts-248, cpts-248/404, or cpts-530/1009 cpts-530/1009 induces
resistance to wild-type RSV A2 challenge 4-6 weeks later.
Passively- Replication of RSV A2 challenge virus.sup.a transferred
Trachea RSV Nasopharynx Peak Virus used for antibodies Chimpanzee
Duration Peak Titer Duration Titer Rhinorrhea Scores immunization
present Number [days] [log.sub.10pfu/ml] [days] [log.sub.10pf-
u/ml] Mean.sup.b Peak cpts-248/404 no .sup. 17.sup.c 0 <0.7 0
<0.7 0 0 no .sup. 18.sup.c 8 3.4 0 <0.7 0 0 yes 21 6 2.7 0
<0.7 0.5 2 yes 22 0 <0.7 0 <0.7 0 0 cpts-530/1009 no 1 7
2.1 0 <0.7 0 0 no 2 0 <0.7 0 <0.7 0 0 yes 23 6 2.5 0
<0.7 0.5 1 yes 24 7 2.0 0 <0.7 0.2 1 cpts-248 no .sup.
25.sup.c 5 2.7 0 <0.7 0 0 no .sup. 26.sup.c 9 1.8 0 <0.7 0 0
yes 29 0 <0.7 0 <0.7 0 0 yes 30 6 2.4 0 <0.7 1.2 3 none no
.sup. 13.sup.d 9 5.1 13 5.4 1.0 1 no .sup. 14.sup.d 9 6.0 8 6.0 1.7
4 no .sup. 15.sup.c 13 5.3 8 2.1 3 no .sup. 16.sup.c 9 5.4 8 5.9
1.0 3 5.6 .sup.aAnimals which were immunized with indicated virus 4
to 6 weeks prior were challenged with 10.sup.4 pfu of RSV A2
wild-type virus. .sup.bMean rhinorrhea scores represent the sum of
scores during the eight days of peak virus shedding divided by
eight .sup.cAnimals from Crowe, et al., Vaccine 12:691-699 [1994].
.sup.dAnimals from Collins, et al., Vaccine 8:164-168 [1990].
EXAMPLE II
Use of Cold Adaptation to Attenuate cpRSV Mutants
This Example describes the introduction of growth restriction
mutations into incompletely attenuated host range-restricted cpRSV
strains by further passage of the strains at increasingly reduced
temperatures to produce derivative strains which are more
satisfactorily attenuated for use in human vaccines.
These cold-adaptation (ca) approaches were used to introduce
further attenuation into the cpRSV 3131 virus, which is
incompletely attenuated in seronegative children.
Under the first strategy, a parent stock of cold-passaged RSV A2
(cpRSV 3131) obtained from Flow Laboratories was prepared by
passage in MRC-5 cells at 25.degree. C. as described in Example 1.
Briefly, cold-passaged virus was inoculated into MRC-5 or Vero cell
monolayer culture at a multiplicity of infection of .gtoreq.0.01
and the infected cells were incubated for 3 to 14 days before
subsequent passage. Virus was passaged over 20 times at
20-22.degree. C. to derive more attenuated virus. The technique of
rapid passage, as soon as the first evidence of virus replication
is evident (i.e., 3 to 5 days), was preferable for selection of
mutants able to replicate efficiently at low temperatures.
Additionally, an RSV subgroup B strain, St. Louis/14617/85 clone
1A1, was isolated in primary African Green monkey kidney cells,
passaged and cloned in MRC cells (1A1-MRC14), and cold-passaged 52
times in MRC-5 or Vero cells at 32 to 22.degree. C.
A second strategy employed a biologically cloned derivative of the
uncloned parental cpRSV 3131 virus. This virus was biologically
cloned in bovine embryonic kidney (BEK) cells [the tissue used to
originally derive the cpRSV 3131 virus--see Friedewald et al., J.
Amer. Med. Assoc. 204:690-694 (1968)]. This cloned virus was then
passaged at 10 day intervals in Vero cells at low temperature.
Alternatively, the cpRSV 3131 virus was cloned by two serial
terminal dilutions (TD2P4) in MRC-5 cells and passaged at 10-day
intervals in MRC-5 or Vero cells.
The third strategy involved selection of mutants that produce large
plaques at low temperature. An RSV 3131 derivative virus designated
plaque D1 that produces large plaques at 25.degree. C. has been
identified. This virus was derived from the third passage (P3)
level of the cp3131-1 (BEK) lineage cp3131-17 (BEK) lineage. The
largest plaque produced by P3 virus was amplified at 32.degree. C.,
then re-plaqued at 25.degree. C. Once again the largest plaque was
selected, amplified, and re-plaqued. After five such cycles, large
placque mutant virus D1 was obtained. D1 was biologically cloned by
two additional cycles of plaque-to-plaque purification at
25.degree. C.
Biologically cloned virus D1 produces distinctly and uniformly
larger plaques at 25.degree. C. than cp3131 or wild-type virus A2.
Thus D1 is cold adapted by the criterion of large plaque size at
25.degree. C. Efficiency of plaque formation studies demonstrated
that D1 is not temperature sensitive. At 37.degree. C., D1 plaques
are indistinguishable from those of wild-type RSV or cp3131,
suggesting that D1 is not restricted in growth at this temperature.
Consistent with this, D1 produces extensive cytopathic effects in
Vero cell monolayers at 37.degree. C. and 40.degree. C. (i.e. the
highest temperatures tested).
EXAMPLE III
Introduction of Further Attenuating Mutations Into ts-RSV
This Example describes the use of ts mutants as parental viruses to
produce more completely attenuated strains. Two RSV A2 ts mutants
were selected for this process, namely ts-4 and ts-1 NG1. Two
distinct methods were chosen to introduce additional mutations into
the RSV ts mutants. First, the incompletely attenuated RSV ts
mutant was subjected to chemical mutagenesis, and mutagenized
progeny that are more temperature-sensitive with regard to plaque
formation were selected for further analysis. Second, the RSV ts
mutants were passaged at low temperature to select RSV nts mutants
with the ca phenotype, i.e., increased capacity to replicate at
suboptimal temperature compared to wild-type parental virus.
A parent stock of ts-1 NG1 virus was prepared from Flow
Laboratories Lot M4 of live Respiratory Syncytial Virus (A-2) ts-1
NG-1 mutant, MRC-5 grown virus. This mutant, derived from the ts-1
mutant by a second round of mutagenesis using nitrosoguanidine,
possesses two or more independent ts mutations, but still induces
substantial rhinorrhea in susceptible chimpanzees. This virus was
passaged twice in Vero cells at 32.degree. C. to create a ts-1 NG-1
suspension for mutagenesis. The virus was then grown in the
presence of 4.times.10.sup.-4M 5-fluorouracil to induce additional
mutations during replication or was exposed to 5-azacytidine at
36.degree. C. after 5--fluorouracil treatment. The mutagenized
stock was then analyzed by plaque assay on Vero cells that were
maintained under an agar overlay, and, after an appropriate
interval of incubation, plaques were identified microscopically.
586 plaques were picked, and the progeny of each plaque were
separately amplified by growth on fresh monolayers of Vero cells.
The contents of each of the tissue cultures inoculated with the
progeny of a single plaque of mutagenized ts-1 NG-1 virus were
separately harvested when cytopathic effects on the Vero cells
appeared maximal. Progeny virus that was more temperature-sensitive
than ts-1 NG1 was sought by titering these plaque pools on HEp2
cells at 32.degree. C. and 36.degree. C. Any virus exhibiting
greater temperature sensitivity than ts-1 NG1 (i.e., 100-fold or
greater reduction in titer at restrictive temperature [36.degree.
C.] compared to 32.degree. C.) was evaluated further. Six plaque
progeny more ts than the tsRSV ts-1 NG-1 parent virus were
identified and these strains were biologically cloned by serial
plaque-purification on Vero cells three times, then amplified on
Vero cells. The cloned strains were titered at 32.degree. C.,
35.degree. C., 36.degree. C., 37.degree. C., and 38.degree. C.
(efficiency of plaque formation assay) to confirm their ts
phenotype. Efficiency of plaque formation data generated by assay
on HEp-2 cells further confirmed the phenotype of the six mutants
(Table 19).
The two most ts viruses, A-20-4 and A-37-8, were highly attenuated
in mice compared to their ts-1 NG1 parent virus, indicating that
acquisition of increased level of temperature sensitivity was
accompanied by augmented attenuation (Table 20). These viruses were
infectious for mice because they induced an antibody response. The
ts-1 NG1/A-20-4 virus is attenuated for chimpanzees (Table 21) and
infection of chimpanzees with ts-1 NG1/A-20-4 induced resistance to
wild-type virus challenge (Table 22). Significantly, rhinorrhea
does not occur.
Mutagenesis of the ts-4 virus was also performed, using the same
method as for mutagenesis of ts-1 NG1, virus. Mutations were also
introduced into the ts-4 viruses by cold-passage. The ts-4 virus
replicates to high titer at 22.degree. C. after 43 cold-passages.
Six plaque progeny that were more ts than the RSV ts-4 parent virus
were identified (Table 23). The ts-4 cp-43 is even further
restricted in replication in Balb/c mice (Table 24).
TABLE-US-00019 TABLE 19 Efficacy of plaque formation of ts-1NG1
derivatives Titer (log.sub.10pfu/ml) at indicated temperature Virus
32.degree. 35.degree. 36.degree. 37.degree. 38.degree.
A-204(4-1).sup.a 5.9* <1 <1 <1 <1 A-37-8(1-2).sup.a 6.3
6.3 <1 <1 <1 A-15-7 3.5 ND 2.1 1.5 <1 A-25-8 5.3 ND
5.0* 4.8* <1 A-21 5.1** ND 4.8** 4.5** <1 Ts1NG1 6.6 6.6 6.5
6.6 <1 .sup.a3.times. plaque purified *Small-plaque phenotype
(<50% wild-type plaque size) **Pinpoint-plaque phenotype
(<10% wild-type plaque size) ND = Not Done
TABLE-US-00020 TABLE 20 Replication of ts-1 NG1 parent and progency
viruses in Balb/c mice Dose Day Post- Titer in Lung Titer in Lung
Virus (log.sub.10pfu) Infection 32.degree. 38.degree. 32.degree.
38.degree- . A2 wt 6.1 4 .sup. 4.66 .+-. 0.32.sup.a 4.80 .+-. 0.16
3.18 .+-. 4.0 3.29 .+-. 0.33 5 5.18 .+-. 0.33 5.25 .+-. 0.23 3.40
.+-. 2.0 3.47 .+-. 0.17 Ts1NG1 5.8 4 4.31 .+-. 0.17 <2.0 2.82
.+-. 0.25 <2.0 5 3.98 .+-. 0.12 <2.0 2.74 .+-. 0.31 <2.0
Ts1NG1/A-20-4 6.1 4 <2.0 <2.0 <2.0 <2.0 5 <2.0
<2.0 <2.0 <2.0 Ts1NG1/A-37-8 6.3 4 <2.0 <2.0 <2.0
<2.0 5 <2.0 <2.0 <2.0 <2.0 .sup.aMean log.sub.10
pfu/g of indicated tissue .+-. standard error. 6 animals/group.
TABLE-US-00021 TABLE 21 Replication of ts-1 NG1/A-20-4, ts-1 NG1,
ts-1 or wild-type RSV A2 in the upper and lower respiratory tract
of seronegative chimpanzees Virus Replication Animal infected
Nasopharynx Trachea with indicated Route of Chimpanzee
Duration.sup.b Peak titer Duration.sup.b Peak titer Rhinorrhea
Scores virus Inoculation.sup.a number [Days] [log.sub.10pfu/ml]
[Days] [log.sub.1- 0pfu/ml] Mean.sup.c Peak ts-1NG1/A-20-4 IN + IT
15 0 <0.7 0 <0.7 0 0 IN + IT 16 0 <0.7 0 <0.7 0 0 IN +
IT 17 0 <0.7 0 <0.7 0 0 IN + IT 18 .sup. 16.sup.d 2.7 0
<0.7 0 0 mean 4.0 mean 1.2 mean 0 mean <0.7 mean 0 mean 0
ts-1 NG1 IN .sup. 19.sup.e 8 4.2 0 <1.1 0.6 1 IN .sup. 20.sup.e
7 3.9 0 <1.1 0.7 1 IN .sup. 21.sup.e 13 5.4 0 <1.1 0.4 1 IN
.sup. 22.sup.e 10 5.2 10d .sup. 3.7.sup.d 0.6 2 mean 9.5 mean 4.7
mean 2.5 mean 1.8 mean 0.6 mean 1.3 tS-1 IN .sup. 23.sup.e 16 3.4 0
<1.1 0.4 1 IN .sup. 24.sup.e 13 4.4 0 <1.1 1.0 3 IN .sup.
25.sup.e 13 5.0 13d 2.2 2.0 4 IN .sup. 26.sup.e 10 3.4 0 <1.1
1.0 2 mean 13 mean 4.1 mean 3.3 mean 1.4 mean 1.1 mean 2.5 A2
wild-type IN .sup. 9.sup.b 9 5.1 13 5.4 1.0 1 IN .sup. 10.sup.b 9
6.0 8 6.0 1.7 4 IN + IT .sup. 11.sup.a 13 5.3 8 5.9 2.1 3 IN + IT
.sup. 12.sup.e 9 5.4 8 5.6 1.0 3 mean 10 mean 5.5 mean 9.3 mean 5.7
mean 1.4 mean 2.8 .sup.aIN = intranasal only; IN + IT = Both
intranasal and intratracheal administration. .sup.bIndicates last
day post-infection on which virus was recovered. .sup.cMean
rhinorrhea score represents the sum of daily scores for a period of
eight days surrounding the peak day of virus shedding, divided by
eight. Four is the highest score; zero is the lowest score.
.sup.dVirus isolated only on day indicated. .sup.eAnimals from
Crowe, et al., Vaccine 11: 1395-1404 [1993].
TABLE-US-00022 TABLE 22 Immunization of chimpanzees with 10.sup.4
pfu of RSV ts-1 NG1/A-20-4, ts-1 NG1, or ts-1 induces resistance to
10.sup.4 pfu RSV A2 wild-type virus challenge on day 28. Virus
Recovery Serum neutralizing Nasopharynx Trachea Rhinorrhea antibody
titer [reciprocal Virus used to Chimpanzee Duration Peak titer
Duration Peak titer scores log.sub.2] on day indicated.sup.b]
immunize animal number [Days] [log.sub.10pfu/ml] [Days]
[log.sub.10pfu/ml]- Mean.sup.a Peak Day 28 Day 49 or 56 ts-1
NG1/A-20-4 15 0 <0.7 0 <0.7 0 0 <3.3 10.7 16 0 <0.7 0
<0.7 0 0 <3.3 11.9 17 0 <0.7 0 <0.7 0 0 5.3 10.3 18 3
2.0 0 <0.7 0 0 8.2 11.8 mean 0.8 mean 1.0 mean 0 mean <0.7
mean 0 mean 0 mean 5.0 mean 11.2 ts-1 NG1 .sup. 19.sup.b 0 <0.7
0 <1.1 0 0 11.1 9.8 .sup. 20.sup.b 0 <0.7 0 <1.1 0 0 12.7
9.1 .sup. 21.sup.b 0 <0.7 0 <1.1 0 0 10.8 11.0 .sup. 22.sup.b
0 <0.7 0 <1.1 0 0 10.0 8.6 mean 0 mean <0.7 mean 0 mean
<1.1 mean 0 mean 0 mean 11.1 mean 9.6 ts-1 .sup. 23.sup.b 0
<0.7 0 <1.1 0 0 9.4 10.5 .sup. 29.sup.b 0 <0.7 0 <1.1 0
0 12.4 12.8 .sup. 25.sup.b 5 0.7 0 <1.1 0 0 9.0 9.6 .sup.
26.sup.b 5 0.7 0 <1.1 0 0 13.4 12.0 mean 2.5 mean 0.7 mean 0
mean <1.1 mean 0 mean 0 mean 11.0 mean 11.2 none .sup. 9.sup.c 9
5.1 13 5.4 1.0 1 <3.3 11.0 .sup. 10.sup.c 9 6.0 8 6.0 1.7 4
<3.3 9.8 .sup. 11.sup.b 13 5.3 8 5.9 2.1 3 <3.3 9.4 .sup.
12.sup.b 9 5.4 8 5.6 1.0 3 <3.3 14.5 mean 10 mean 5.5 mean 9.3
mean 5.7 mean 1.5 mean 2.8 mean <3.3 mean 11.1 .sup.aMean
rhinorrhea score represents the sum of scores during the eight days
of peak virus shedding divided by eight. Four is the highest score;
zero is the lowest score. .sup.bAnimals from Crowe, et al., Vaccine
11: 1395-1404 [1993]. .sup.cAnimals from Collins, et al., Vaccine
8: 164-168 [1990]. .sup.dSerum neutralizing titers in this table
were determined in a new assay simultaneously with other specimens
represented in the table.
TABLE-US-00023 TABLE 23 The efficiency of plaque formation of six
mutants derived from RSV ts-4 and tested in HEp-2 cells at
permissive and restrictive temperatures, compared with controls.
The titer of virus [log.sub.10pfu/ml] Small- Shut-off at the
indicated temperature [.degree. C.] plaques temperature Virus 32 33
34 35 36 37 38 39 40 at 32.degree. C. [.degree. C.].sup.1 A2
wild-type 5.7 5.8 5.5 5.5 5.3 5.5 5.5 5.4 5.5 no >40 ts-4 4.5
4.7 4.4 4.7 4.7 4.1 3.7 3.0 2.5 no 40 ts-4 cp-43 6.2 6.1 6.1 6.0
4.4* 4.2** 1.7** <0.7** <0.7 no 37 ts-4/20.7.1 6.0 5.9 5.7
5.7* 4.5** 1.8 <0.7 <0.7 <0.7 no 37 ts-4/19.1.2 5.8 5.7
5.5 5.6* 4.4** <0.7 <0.7 <0.7 <0.7 no 37 ts-4/15.8.2
5.3* 5.4* 4.8* 4.9* 2.8** <0.7 <0.7 <0.7 <0.7 yes - 36
ts-4/29.7.4 5.7 5.6 5.6 5.7* <0.7 <0.7 <0.7 <0.7
<0.7 no 36- ts-4/31.2.4 4.7 4.2 4.1 4.0* <0.7 <0.7 <0.7
<0.7 <0.7 no 36- .sup.1Shut-off temperature is defined as the
lowest restrictive temperature at which a 100-fold or greater
reduction of plaque titer is observed [bold figures in table].
*Small-plaque phenotype [<50% wild-type plaque size]
**Pinpoint-plaque phenotype [<10% wild-type plaque size]
TABLE-US-00024 TABLE 24 Replication of RSV ts-4 and RSV ts-4 cp-43
in Balb/c mice.sup.1 Virus titer (mean log.sub.10pfu/g tissue of
six animals .+-. standard error) Shutoff Virus used to temperature
of infect animals: virus (C. .degree.) Nasal turbinates Lungs A2
wild-type >40 5.0 .+-. 0.14 5.2 .+-. 0.05 ts-4 39 4.3 .+-. 0.09
4.7 .+-. 0.11 ts-4 cp-43 37 2.1 .+-. 0.09 2.7 .+-. 0.27 .sup.1Mice
were administered 10.sup.6.3p.f.u. intranasally under light
anesthesia on day 0, then sacrificed by CO.sub.2 asphyxiation on
day 4.
EXAMPLE IV
RSV Subgroup B Vaccine Candidates
This Example describes the development of RSV subgroup B virus
vaccine candidates. The same approach used for the development of
the subgroup A mutants of the invention was utilized for the
subgroup B viruses. A parent stock of wild-type B-1 RS virus was
cold-passaged 52 times in Vero cells at low temperature
(20-25.degree. C.) and the virus was subjected to plaque
purification at passages 19 and 52. Three of the clones derived
from the passage 52 suspension were evaluated independently, and
one clone, designated RSV B-1cp52/2B5, was selected for further
evaluation because it was highly attenuated in the upper and lower
respiratory tract of the cotton rat (Table 25). An evaluation of
several clones at different passage levels of the cp RSV B-1 virus
indicate that the RSV B-1cp52/2B5 mutant sustained multiple
mutations that independently contribute to its attenuation
phenotype. The RSV B-1cp52/2B5 mutant retained its attenuation
phenotype following prolonged replication in immunosuppressed
cotton rats (Table 26). This finding of a high level of genetic
stability is consistent with the fact that it possesses three
mutations contributing to the attenuation phenotype.
Further evaluation of the subgroup B mutants in order to
characterize them in a similar manner as the subgroup A mutants,
was carried out in Caribbean Green monkeys (Tables 27 and 28) and
chimpanzees (Table 29). Monkeys immunized with either RSV B-1 cp-23
or cp52/2B5 were resistant to replication of RSV B-1 wild-type
virus, indicating that infection with the highly attenuated
derivatives of the RSV B-1 wild-type virus was sufficient to induce
resistance to wild-type challenge (Table 27).
The results in the seronegative chimpanzee, like that in the Green
monkeys, clearly evidence the attenuation of the RSV B-1cp52/2B5 in
the upper and lower respiratory tracts.
The RSV B-152/2B5 mutant has been further mutagenized with
5-fluorouracil and the resulting plaques picked and screened at
32.degree. vs. 38.degree. C. for the ts phenotype. The selected
cpts mutants were plaque-purified three times in Vero cells and
then amplified twice in Vero cells. As a result, seven cpts mutants
of RSV B-1cp52/2B5 have been identified (Table 30) and their level
of replication in cotton rats has been studied (Table 31). One of
these mutants, namely cpts176, was further mutagenized and a series
of mutant derivatives were obtained that were more ts in vitro than
the RSV B-1cpts 176 parent virus (Table 32).
As with the subgroup A mutants of the invention, the subgroup B
mutants are infectious and exhibit a significant degree of
attenuation for cotton rats, monkeys, and chimpanzees. Despite
attenuation in vivo, the RSV B-1 cp mutant viruses induced
resistance in monkeys against wild-type challenge. The ts mutants
of the RSV B-1 cpts52/2B5 virus are attenuated and demonstrate a
more restricted level of replication in the nasopharynx and lungs
of the cotton rat than the RSV B-1 52/2B5 parent virus.
TABLE-US-00025 TABLE 25 Replication in cotton rats of RSV B-1
wild-type compared with five plaque-purified cold-passaged mutants
derived from RSV B-1, in two separate experiments. Virus recovery
(log.sub.10pfu/g tissue) on day 4* Virus used to infect Nasal
turbinates Lungs animals on day 0** Exp. 1 Exp. 2 Exp. 1 Exp. 2 RSV
B-1 wild-type 4.7 .+-. 0.14 5.1 .+-. 0.10 5.4 .+-. 0.15 5.8 .+-.
0.08 RSV B-1 cp-12/B1A nd 3.3 .+-. 0.15 nd 4.4 .+-. 0.10 RSV B-1
cp-23 nd 2.4 .+-. 0.36 nd 3.2 .+-. 0.31 RSV B-1 cpsp-52/1A1 1.7
.+-. 0.11 2.1 .+-. 0.27 3.0 .+-. 0.13 2.3 .+-. 0.07 RSV B-1
cp-52/2B5 1.8 .+-. 0.25 2.2 .+-. 0.3 1.8 .+-. 0.11 1.5 RSV B-1
cp-52/3C1 1.8 .+-. 0.14 nd 1.8 .+-. 0.14 nd RSV A2 5.9 .+-. 0.09
5.4 .+-. 0.07 6.6 .+-. 0.06 6.1 .+-. 0.06 RSV A2 cpts530/1009 3.2
.+-. 0.11 2.1 .+-. 0.22 2.1 .+-. 0.19 1.7 .+-. 0.12 *Virus recovery
determined by titration of tissue homogenates on Vero cell
monolayer cultures at 32.degree. C. with a 10-day incubation in
Experiment 1, 7-day incubation in Experiment 2. **Cotton rats
infected intranasally with 10.sup.5.5 pfu of indicated virus. nd =
not done
TABLE-US-00026 TABLE 26 Growth in cotton rats of day 14 isolaes*
from RSV B-1 cp52/2B5 infected immunosuppressed cotton rats
compared with controls Virus Recovery Virus titer on day 4 in
indicated tissue RSV B-1 wild-type Virus (mean log.sub.10pfu/g
tissue .+-. log.sub.10pfu/g) infected standard error of the mean)
Nasal animals.sup.a Nasal turbinates.sup.b Lungs.sup.c turbinates
Lungs RSV B-1 3.9 .+-. 0.03 (6/6) 4.8 .+-. 0.12 (6/6) -- --
wild-type RSV B-1 2.0 .+-. 0.07 (8/8) <1.5 (0/8) 1.9 >3.3 cp
52/2B5 isolate 1 1.5 .+-. 0.13 (5/8) 1.5 .+-. 0.04 (1/8) 2.5 3.3
isolate 2 1.5 .+-. 0.13 (6/8) <1.5 (0/8) 2.4 >3.3 isolate 3
1.5 .+-. 0.16 (3/8) <1.5 (0/8) 2.5 >3.3 isolate 4 1.3 .+-.
0.09 (4/8) <1.5 (0/8) 2.6 >3.3 isolate 5 1.2 .+-. 0.00 (2/8)
<1.5 (0/8) 2.7 >3.3 isolate 6 1.2 .+-. 0.00 (3/8) <1.5
(0/8) 2.7 >3.3 isolate 7 1.3 .+-. 0.06 (3/8) <1.5 (0.8) 2.7
>3.3 *Isolates were virus suspensions obtained following
amplification by one Vero cell tissue culture passage of virus
present in the original nasal turbinate homogenate on day 14 of an
immunosuppressed cotton rat. .sup.aGroups of 8 cotton rats infected
with 10.sup.5.5 pfu of indicated virus in a 0.1 ml inoculum on day
0. .sup.b( ) indicates the numbers of animals from which virus was
detected at 1.2 log.sub.10pfu/g or greater. .sup.c( ) indicates the
numbers of animals from which virus was detected at 1.5
log.sub.10pfu/g or greater.
TABLE-US-00027 TABLE 27 Replication in Caribbean Green monkeys of
RSV A2 and RSV B-1 wild-types compared with that of two
cold-passaged mutants derived from RSV B-1, followed by homologous
or heterologous RSV A2 or B-1 wild-type challenge Immunization
Challenge Virus used to infect NP swab Tracheal Lavage NP swab
Tracheal Lavage animals on day 0.sup.a Peak titer.sup.b Days
shed.sup.b Peak titer Days shed Challenge virus Peak titer.sup.b
Peak titer.sup.b A2 3.4 9 <0.7 0 A2 <0.7 <0.7 3.5 7
<0.7 0 A2 <0.7 <0.7 3.5 9 4.8 10 A2 <0.7 <0.7 3.2 8
0.7 7 A2 <0.7 <0.7 1.7 6 <0.7 0 B-1 <0.7 <0.7 3.5 10
<0.7 0 B-1 <0.7 <0.7 2.4 8 0.7 0 B-1 <0.7 <0.7 4.2 9
<0.7 0 B-1 <0.7 <0.7 mean 3.2 mean 8.3 mean 1.2 B-1 2.8 9
1.5 10* B-1 <0.7 <0.7 2.3 9 1.9 7 B-1 <0.7 <0.7 2.2 7
1.7 10* B-1 <0.7 <0.7 2.2 9 1.3 10* B-1 <0.7 <0.7 1.6
8* 1.2 5* A2 <0.7 <0.7 2.1 10 1.7 7* A2 <0.7 <0.7 mean
2.2 mean 8.7 mean 1.6 mean <0.7 mean <0.7 B-1 cp-23 1.8 14
<0.7 0 B-1 <0.7 <0.7 1.3 5 <0.7 0 B-1 <0.7 <0.7
2.0 8 0.7 10 B-1 <0.7 <0.7 1.7 4 <0.7 0 B-1 <0.7
<0.7 mean 1.7 mean 7.8 mean <0.7 mean <0.7 mean <0.7
B-1 cp-52 1.3 8 <0.7 0 B-1 <0.7 <0.7 1.3 4 <0.7 0 B-1
<0.7 <0.7 1.3 7 <0.7 0 B-1 <0.7 <0.7 0.7 3* <0.7
0 B-1 <0.7 <0.7 mean 1.2 mean 5.5 mean <0.7 mean <0.7
mean <0.7 .sup.aAnimals infected intratracheally and
intranasally with 10.sup.5.5 p.f.u. virus at each site in a 1.0 ml
inoculum on day 0. .sup.bLog.sub.10pfu/ml titers determined by
plaque assay on HEp-2 cell monolayer cultures for RSV A2, and Vero
cell monolayer cultures for RSV B-1 and its derivatives. *Virus
detected only on day indicated.
TABLE-US-00028 TABLE 28 Neutralizing antibody response of Caribbean
Green Monkeys infected with RSV A2, RSV B-1, or B-1 cpderivatives,
then challenged with homologous or heterologous wild-type virus one
month later. Animals infected on 60% Plaque reduction serum
neutralizing titer against day 0 with Day 28 indicated virus
[reciprocal mean] indicated virus challenge RSV A2 RSV B-1 [number
of virus [number Post-infection Post-challenge Post-infection
Post-challenge animals] of animals] Day 0 [day 28] [day 56] Day 0
[day 28] [day 56] A2 [8] A2 [4] <10 53,232 40,342 <10 1,552
1,911 B-1 [4] 23,170 1,911 B-1 [6] B-1 [4] <10 3,327 3,822
<10 2,048 2,521 A2 [2] 30,574 35,120 B-1 cp23[4] B-1 [4] <10
6,208 10,086 <10 4,705 7,132 B-1 cp-52/2B5 [4] B-1 [4] <10
194 16,384 <10 239 3,822
TABLE-US-00029 TABLE 29 The replication of RSV B-1 or RSV B-1 cp-52
in seronegative chimpanzees following simultaneous intratracheal
and intranasal administration..sup.a Virus replication Nasopharynx
Trachea Animal infected with indicated Infection Duration.sup.b
Peak titer Duration.sup.b Peak titer Rhinorrhea score virus on day
0 dose [pfu] Exp. [days] [log.sub.10pfu/ml] [days]
[log.sub.10pfu/ml] Peak Mean.- sup.c RSV B-1 wild-type 10.sup.4 1 9
3.7 8 3.2 1 0.5 1 10 3.5 0 <0.7 2 0.9 1 10 2.8 0 <0.7 3 1.1 1
10 2.7 8 3.4 3 0.9 avg. 9.8 mean 3.2 avg. 4.0 mean 2.0 mean 2.3
mean 0.9 10.sup.5 2 7 2.8 8 1.0 1 1.0 2 7 3.3 4 3.9 3 1.3 avg. 7.5
mean 3.1 avg. 6.0 mean 2.5 mean 2.0 mean 1.1 B-1 cp-52/2B5 10.sup.4
1 5 1.5 0 <0.7 0 0 1 0 <0.7 0 <0.7 0 0 10.sup.5 3 0
<0.7 0 <0.7 0 0 3 0 <0.7 0 <0.7 0 0 avg. 1.2 mean 0.9
mean 0 mean <0.7 mean 0 mean 0 .sup.aThese data were combined
from three separate experiments, the infection dose of indicated
virus in the first experiment was 10.sup.4, the second and third
experiments were 10.sup.5. .sup.bIndicates the last day
post-infection on which virus was recovered. .sup.cMean rhinorrhea
score represents the sum of daily scores for a period of eight days
surrounding the peak day of virus shedding, divided by eight. Four
is the highest score; zero is the lowest score.
TABLE-US-00030 TABLE 30 The efficiency of plaque formation of eight
mutants derived from RSV B-1 cp52/2B5 Plaque titer
(log.sub.10pfu/ml in Vero of HEp-2 Cells at indicated temperatures
(.degree. C.) HEp-2 Vero HEp-2 Shutoff RVS 32 32 35 36 37 38 39
temp (.degree. C.) B-1 wild-type 6.1 5.8 5.7 5.6 5.6 5.7 5.5 >39
B-1 cp52/2B5 5.9 5.4 5.2 5.1 5.0 5.0 4.7** >39 cpts452 6.1 5.6
5.2 5.2 3.3** 3.1** <0.7 37 cpts1229 5.7 5.1 4.9 5.1 4.4**
<0.7 <0.7 38 cpts1091 5.7 5.1* 4.7** 5.2** <0.7 <0.7
<0.7 37 cpts784 5.1 4.3* 4.0** 4.1** <0.7 <0.7 <0.7 37
cpts176 6.1 5.4* 4.8* 5.0** <0.7 <0.7 <0.7 37
cptssp1415.sup.a 5.8 <0.7 <0.7 <0.7 <0.7 <0.7
<0.7 38 cpts1324 5.9 5.1 5.0* 5.0 <0.7 <0.7 <0.7 37
cpts1313 5.7 3.9** 3.0** <0.7 <0.7 <0.7 <0.7 36 AS 6.4
6.3 6.3 6.3 6.3 6.3 6.3 >39 A2/248 6.3 6.3 6.2 6.3 5.8 <0.7
<0.7 38 A2/248/404 4.4 4.3 3.3 4.0 <0.7 <0.7 <0.7 37
A2/248/955 4.8 4.8 4.8 4.4 <0.7 <0.7 <0.7 37 *Small-plaque
phenotype (<50% wild-type plaque size). **Pinpoint-plaque
phenotype (<10% wild-type plaque size). .sup.aAt 32.degree. C.,
no plaques were observed. Therefore, no shut-off temperature was
determined by efficiency of plaque formation. The mutant was
assigned a shutoff temperature of 38.degree. C. in HEp-2 cell
culture as determined by a 100-fold decrease in virus yield
(TCID.sub.50) in liquid medium overlay. Bold figures denote shutoff
temperatures (defined as the lowest restrictive temperature at
which a 100-fold or greater reduction of plaque titer was
observed).
TABLE-US-00031 TABLE 31 Level of replication in cotton rats of
seven ts mutants derived from RSV B-1 cp-52/2B5 Replication in
cotton rats.sup.1 (mean log.sub.10pfu/g tissue of six animals .+-.
s.e.) RSV Nasal turbinates Lungs B-1 wild-type 4.3 .+-. 0.05
(6/6).sup.2 4.4 .+-. 0.25 (6/6) B-1 cp52/2B5 1.7 .+-. 0.11 (6/6)
<1.5 (0/6) cpts452 1.4 .+-. 0.1 (3/6) <1.5 (0/6) cpts1091 1.7
.+-. 0.07 (4/6) <1.5 (0/6) cpts784 1.5 (1/6) <1.5 (0/6)
cpts1229 1.4 .+-. 0.15 (3/6) <1.5 (0/6) cptsl76 1.5 .+-. 0.17
(3/6) <1.5 (0/6) cptssp1415 <1.2 (0/6) <1.5 (0/6) cpts1324
<1.2 (0/6) <1.5 (0/6) .sup.1Cotton rats were inoculated
intranasally with 4.5-5.8 log.sub.10pfu under light anesthesia on
day 0, then sacrificed by CO.sub.2 asphyxiation on day 4.
.sup.2Titer from samples containing virus only. Parenthesis
indicate fraction of samples containing virus.
TABLE-US-00032 TABLE 32 The efficiency of plaque formation of 14
mutants derived from RSV B-1 cpts176, compared with controls In
vitro efficiency of plaque formation in HEp-2 cell monolayer
culture The titer of virus (log.sub.10pfu/ml) Shut-off at the
indicated temperature (.degree. C.) temperature RSV 32 35 36 37
(.degree. C.).sup.1 B-1 5.6 5.5 5.4 5.3 >39 wild-type B-1 5.7
5.7 5.6 5.3 >39 cp52/2B5 B-1 5.5 3.5 3.0 1.9 36/37 cpts176
176/645 3.8 3.0 2.6** <0.7 37 176/860 3.1 2.5 2.4 <0.7 37
176/196 3.3 2.5 2.0** <0.7 37 176/219 2.6 2.3 2.0** <0.7 37
176/18 4.0 3.2 <0.7 <0.7 36 176/73 2.6 2.0 <0.7 <0.7 36
176/1072 3.2 2.3 <0.7 <0.7 36 176/1038 2.8 2.2 <0.7
<0.7 36 176/81 2.2 2.0 <0.7 <0.7 36 176/1040 3.2 2.0
<0.7 <0.7 36 176/1045 2.5 1.9 <0.7 <0.7 36 176/517 3.1
2.0** <0.7 <0.7 36 176/273 2.3 <0.7 <0.7 <0.7 35
176/427 3.5 <0.7 <0.7 <0.7 35 **Pinpoint-plaque phenotype
(<10% wild-type plaque size) .sup.1Shut-off temperature is
defined as the lowest restrictive temperature at which a 100-fold
or greater reduction of plaque titer is observed (bold figures in
table).
To aid in the evaluation and manipulation of RSV B subgroup vaccine
candidates, the complete nucleotide sequence of the wild-type B-1
virus has been determined [SEQ ID NO:2]. This sequence was compared
with the sequence of the attenuated B-1 derivative, cp-52/2B5
(cp-52), described above. This sequence analysis revealed a large
deletion in cp-52 spanning most of the SH and G genes, with no
predicted ORF for either gene. More specifically, most of the
region spanning the SH and G genes of the cp-52 virus was deleted,
retaining only the SH gene-start signal and a portion of the 3'
(downstream) end of the G gene and its gene-end signal. The
remaining SH:G region could encode a chimeric transcript of
.about.91 nucleotides with no ORF. Northern blot analysis of cp-52
confirmed that multiple unique polytranscripts contained SH:G
read-through mRNAs, consistent with a deletion mutation spanning
the SH:G gene junction. Western blot and immunostain assays
confirmed that intact G glycoprotein was not produced by the cp-52
virus. In addition to the long deletion, cp-52 virus contains seven
nucleotide differences (Table 33), five of which are coding changes
(one in the F gene and four in the L gene), one is silent (F gene),
and one is in the noncoding G:F intergenic region. Importantly,
this RSV mutant remains highly infectious in tissue culture despite
the absence of SH and G proteins. These data identify a novel class
of replication competent deletion mutants which provide for
alternative or combinatorial approaches to developing recombinant
RSV vaccine candidates.
TABLE-US-00033 TABLE 33 Sequence comparison of RSV B1 and cp-52
Amino acid change Genomic Nucleotide* (#) Gene position B1
cp-52.dagger. B1.fwdarw.cp-52 G/F 5626 C A** non-coding intergenic
F 6318 A G Glu.fwdarw.Gly (218) 6460 U C** silent (265) L 10973 G A
Arg.fwdarw.Lys (822) 13492 A C Asn.fwdarw.His (1662) 14164 U A**
Leu.fwdarw.Ile (1886) 14596 U C** Phe.fwdarw.Leu (2030) *Positive
(+) sense. .dagger.Nucleotide position 4249-5540 spanning the SH
and G genes is deleted in cp-52. **Mutations present in cp-23
Other subgroup B mutants isolated at different passage levels in
the cp-52 passage history incorporate various of the cp-52
mutations, depending on passage level (Table 34). Exemplary
subgroup B mutants in this context include RSV B-1 cp-12, RSV B-1
cp-23, RSV B-1 cp-32, RSV B-1 cp-42. Table 34 depicts (as negative
sense) the distribution of these specific mutations among exemplary
B subgroup mutants. This varied distribution of mutations allows
for more refined characterization of the attenuating effects of
these mutations in the designated strains. For example, cp-23
incorporates the mutations at nucleotide positions 5626, 6460,
14164 and 14596 found in cp-52 (Table 34), but has no differences
from the parental B-1 wild-type strain in the SH and G gene region
that is deleted in cp-52. cp-42 incorporates the same SH and G
deletion as cp-52, while cp32 presents a distinct deletion of
sequences within the SH and G genes.
TABLE-US-00034 TABLE 34 Sequence comparison between RSVB1,
RSVB1cp12, cp 23, cp32, cp 42, and cp 52 Nucleotide Changes genome
(-) sense Nucl. RSVB1 RSVB1 RSVB1 RSVB1 RSVB1 Amino Acid Gene Pos.
RSVB1 CP12 .cndot..cndot.CP23 CP32 CP42 .cndot.CP52 Changes G/F
5626 G G T T *ND T non-coding lGr F 6318 T ND T T ND C
Glu.fwdarw.Gly (218) 6460 A A G G *ND G silent (265) L 10973 C ND C
C T T Arg.fwdarw.Lys (822) 13492 T ND T T T G Asn.fwdarw.His (1662)
14164 A A T T T T Leu.fwdarw.Ile (1886) 14596 A G G G G G
Phe.fwdarw.**Leu (2030) .cndot.Nucleotide region (position
4249-5540) spanning the SH and G genes is deleted in cp52.
.cndot..cndot.No nucleotide differences from B1 parent found in the
SH and G gene region which is deleted in cp52. *These nucleotides
are most likely the same as in cp23 and cp 52. **A Leucine at amino
acid position 2030 in the L polymerase is also found in RSV2B.
EXAMPLE V
Bivalent RSV Subgroup A and B Vaccine
Studies with subgroup A and B viruses demonstrate that in vitro, no
interference occurs between wild-type A2 and B-1 viruses, nor
between cpts530/1009 and RSV B-1 cp52/2B5 derivatives in Vero cell
monolayer cultures. The in vivo results of bivalent infection in
cotton rats are presented in Table 34. These results confirm the in
vitro results, which show no interference between A-2 and B-1
wild-type RSV, and cpts530/1009 and RSV B-1 cp52/2B5. It is
expected, therefore, that each vaccine virus will induce homotypic
immunity against wild-type virus, since each component of the
bivalent vaccine replicates to a level in the dual infection
comparable to that seen during single infection. Each virus alone
is capable of inducing homotypic resistance against RSV wild-type
challenge.
TABLE-US-00035 TABLE 35 Bivalent infection of cotton rats with RSV
A2 and RSV B-1 viruses or mutant derivatives indicates no in vivo
interference Virus recovery from indicated tissue (log.sub.10pfu/g)
Nasal turbinates Lungs Viruses used to RSV A RSV B RSV A RSV B
infect animals* titer titer titer titer A2 5.4 .+-. 0.08 -- 5.8
.+-. 0.07 -- B-1 -- 4.6 .+-. 0.03 -- 5.4 .+-. 0.12 A2 + B-1 5.2
.+-. 0.11 3.6 .+-. 0.07 5.7 .+-. 0.08 5.0 .+-. 0.05 A2 cpts530/1009
3.2 .+-. 0.09 -- 1.9 .+-. 0.15 -- B-1 cp52 -- 2.4 .+-. 0.08 --
<1.5 A2 cpts530/1009 + 2.8 .+-. 0.13 2.0 .+-. 0.14 1.8 .+-. 0.08
<1.5 B1 cp-52 *Groups of six animals infected with 10.sup.5 pfu
intranasally on day 0 in a 0.1 ml inoculum.
EXAMPLE VI
A Single Mutation in Polymerase (L) Gene Elicits ts Phenotype
This Example describes the specific mutations in the polymerase
gene (L) that were produced by chemical mutagenesis of incompletely
attenuated host range-restricted cpRSV to produce ts strains,
cpts248 and cpts530, which are more highly attenuated and suitable
for use in RSV vaccine preparations. As described in the Examples
above, cpts248 has been found to be attenuated, immunogenic, and
fully protective against wild-type challenge in seronegative
chimpanzees and is more stable genetically during in vivo
replication than previously evaluated tsRSV mutants. As described
above, the cpts248 strain was subjected to chemical mutagenesis to
further reduce residual reactogenicity, yielding a series of
mutants with increased temperature sensitivity or small plaque
phenotype, including cpts248/404. In a like manner, cpts530/1009
was derived from cpts530.
The genetic bases for increased attenuation and ts phenotype of
cpts248 and cpts530 were determined by comparing the complete
genomic sequence of these viruses with that of the previously
determined sequence of the cpRSV parental virus. The complete
nucleotide sequence of cpRSV was determined and compared with that
of RSV A2 wild-type virus (a laboratory strain which was not part
of the direct passage lineage), as well as with the sequence of its
low passaged wild-type parent virus (RSV A2/HEK7). The cpRSV
differs from its RSV A2/HEK7 parent virus by five nucleotide
changes, one in the nucleoprotein (N), two in the fusion protein
(F) gene and two in the polymerase (L) gene. The complete 15,222
nucleotide sequence and amino acid sequence of cpts248,
cpts248/404, cpts530, cpts530/1009, and cpts530/1030 were
determined.
The derivation of the RSV mutants cpts248 and cpts530 from their
cpRSV parent by random chemical mutagenesis was described in
Example 1. The virus suspension used for infecting cells for
production of virus to be used as a source of purified viral RNA
was a clarified tissue culture supernatant containing virus that
had been passaged four times in liquid medium in Vero cell
monolayer culture following biological cloning (i.e., three
plaque-to-plaque passages in Vero cell monolayers under agar).
Cell monolayers were infected at a multiplicity of infection (moi)
of 0.1 with cpts248, cpts248/404, cpts530, cpts530/1009, or
cpts530/1030 viruses. Total RNA was prepared from infected cell
monolayers when moderate CPE was observed (average of 4-5 days
postinfection). The supernatant fluid was removed by aspiration,
and infected cell monolayers were harvested by lysis with
guanidinium isothiocynanate, followed by phenol-chloroform
extraction. RNA was reverse transcribed using Superscript II TM
reverse transcriptase (Life Technologies) random hexamer primers,
and reaction conditions as described in protocols supplied by the
manufacturer.
The resulting cDNA was separated from primers using TE-100 spin
columns (Clontech, Palo Alto, Calif.) and used as template in
polymerase chain reactions (PCR) to generate a series of ten
overlapping cDNA clones spanning the entire RSV genome. The
oligonucleotide primers for PCR were designed from the nucleotide
sequence of the prototype A2 virus (Mink et al., Virology
185:615-624 (1991); Stec et al., Virology 183:273-287 (1991);
Collins et al., Proc. Natl. Acad. Sci. U.S.A. 88:9663-9667 (1991);
Connors et al., Virology 208:478-484 (1995)), and had been
demonstrated previously to amplify both the RSV A2 wild-type virus
and its derivative, the cpRSV parental virus. Uracil-containing
oligonucleotide primers were used for cloning RSV sequences into
the pAMP1 vector using the CloneAmp uracil DNA glycosylase system
(Life Technologies). PCR reactions were performed according to the
manufacturer's protocols (Perkin-Elmer, Norwalk, Conn.) and carried
out for 34 cycles of each 1 min. at 92.5.degree. C., 1 min. at
55.degree. C., and 3 min. at 72.degree. C. Each fragment was
electrophoresed in a 1% agarose/TAE gel, recovered by the Geneclean
II System (Bio101, Vista, Calif.), and cloned into the pAMP1
vector. Two or more separate clones of each fragment were generated
from separate PCR reactions. For analysis of the 3' leader region,
viral RNA (vRNA) was polyadenylated as described in Mink et al.,
Virology 185:615-624 (1991) in a 50 .mu.l reaction. Following
incubation at 37.degree. C. for 10 minutes, the reaction was
stopped with 2 .mu.l of 0.5 M EDTA. The polyadenylated RNA product
was purified by extraction with phenol chloroform and ethanol
precipitation, and then reverse transcribed into cDNA, amplified by
PCR, and cloned using a rapid amplification by the 3' RACE system
(Life Technologies). Similarly, for analysis of the 5' trailer
region, vRNA was reverse transcribed into cDNA, tailed using
terminal deoxynucleotidyl transferase and dCTP, column purified,
made double-stranded and amplified by PCR, and cloned using a 5'
RACE system (Life Technologies).
Cloned cDNAs for cpts248 were sequenced from double stranded
plasmids by the dideoxynucleotide method using synthetic
oligonucleotide primers (either plasmid primers or RSV specific
primers), [.alpha..sup.35S]DATP and Sequenase 2.0 (United States
Biochemicals, Cleveland, Ohio). Differences between the observed
sequences and those of the previously published parental virus
cpRSV were confirmed by sequencing two or more clones in both
forward and reverse directions, and by sequencing uncloned PCR
products.
Nucleotide sequences of the cpts248/404, cptsS30, cpts530/1009, and
cpts530/1030 were determined using a different technique. Three to
ten overlapping cDNA clones representing the genome of cptsRSV
mutant virus were generated by RT-PCR of total infected-cell RNA or
vRNA. The complete nucleotide sequence of each clone was determined
by automated DNA sequence at the NCI Frederick Cancer (Frederick,
Md.) using Taq kit (ABI, Foster City, Calif.) on a M13 sonicated
random library constructed in phage M13 for each plasmid insert.
Both strands were sequenced and differences between the cpRSV and
the cptsRSV mutant sequences were confirmed by manual sequencing
(as above) of a second independently derived RT-PCR product using
Sequenase 2.0 (USB, Cleveland, Ohio). The 3'- and 5'-end sequences
were determined as described above.
The complete nucleotide sequence of the 15,222-nucleotide RNA
genome of the cpts248, cpts248/404, cpts530, cpts530/1009, and
cpts530/1030 strains were determined. Changes relative to the
published sequences of the cpRSV and RSV A2/HEK7 (wild-type)
parental viruses (Conners et al., Virology 208:478-484 (1995)) were
confirmed on independently derived cDNA clones of these cptsRSV
mutants, and were rechecked in the cpRSV virus by sequencing an
additional clone of cpRSV. An ambiguity in the sequence of the
cpRSV virus (compared with the A2/HEK7 wild-type virus) was
identified. The ambiguity occurred at position 1,938 from the 3'
end of the negative sense genome and consisted of nucleotide
heterogeneity (G or A in positive sense) that would be predicted to
encode an amino acid change (Val or Ile) at amino acid position 267
of the 391 amino acid-nucleocapsid (N) protein. Thus, the cpRSV
actually consisted of a mixed population of viruses. This accounts
for the initial failure to detect the change at position 1938 in
Conners et al., supra. A virus with the A mutation at position
1,938 was the immediate parent of the cpts248 derivative as well as
of the cpts530 sister clone. Thus, the cpRSV which was the
immediate parent virus of the cpts derivative contains five amino
acid differences from its A2/HEK parent.
A single nucleotide difference between the cpRSV and cpts248
mutants was found at nucleotide position 10,989 (an A to T change)
(Table 36). This mutation occurred within the polymerase (L)
translation open reading frame, encoding a predicted amino acid
change of gin to leu at amino acid position 831 in the 2,165 amino
acid L protein. The cpts248/404 mutant possesses two nucleotide
differences from its cpts248 parent, one at nucleotide 12,046 (T to
A) in the L gene, and one at nucleotide 7605 (T to C) in the
transcription start signal sequence of the M2 gene. The nucleotide
substitution in the L gene resulted in an amino acid change from
asp to glu at position 1183 in the L protein. Thus after two
independent rounds of mutagenesis of cpRSV, the cpts248/404 virus
acquired two nucleotide changes in the L gene (corresponding to two
amino acid substitutions) and one nucleotide change in the
transcription start signal of the M2 gene. Compared to its
wild-type progenitor, A2/HEK7, the cpts248/404 mutant differs in
seven amino acids (four in L, two in F, and one in N) and in one
nucleotide in the transcription start signal of the M2 gene.
TABLE-US-00036 TABLE 36 Nucleotide Sequence Differences among
cp-RSV, cpts-248, cpts-248/404 mutant viruses Nucleotide and Amino
Acid Change Nucleo- Amino A2 wt cpts- tide.sup.1 Acid Gene (HEK-7)
cp-RSV cpts-248 248/404 1938 267 N G (val) A (ile) A (ile) A (ile)
3242 P A A A AA.sup.2 6313 218 F A (glu) C (ala) C (ala) C (ala)
7228 523 F C (thr) T (ile) T (ile) T (ile) 7605 Gene Start T T T C
(M2) 9453 319 L G (cys) A (tyr) A (tyr) A (tyr) 10989 831 L A (gln)
A (gln) T (leu) T (leu) 12046 1183 L T (asp) T (asp) T (asp) A
(glu) 13565 1690 L C (his) T (tyr) T (tyr) T (tyr) .sup.1Positive
sense .sup.2Increases genome length by 1 nucleotide.
The cpts530 differs from the parental strain cpRSV by the single
additional nucleotide substitution of C to A at position 10,060 and
results in a phe to leu amino acid change at position 521 of the L
protein (Table 37). The cpts530/1009 mutant has a single nucleotide
substitution at nucleotide 12,002 (A to G) resulting in a met to
val substitution at amino acid 1169 of the L protein. Compared to
its wild-type progenitor, A2/HEK7, the cpts530/1009 mutant differs
in seven amino acids (four in L, two in F, and one in N).
The cpts530/1030 mutant has a single additional nucleotide
substitution at nucleotide 12458 (T to A) resulting in a Tyr to Asn
substitution at amino acid 1321 of the L protein. Compared to its
wt progenitor, A2/HEK, the cpts530/1030 mutant differs in seven
amino acids (four in L, two in F, and one in N).
TABLE-US-00037 TABLE 37 Nucleotide Sequence Differences among
cp-RSV, cpts-530, cpts-530/1009 mutant viruses Nucleotide and Amino
Acid Change Nucleo- Amino A2 wt cpts- tide.sup.1 Acid Gene (HEK-7)
cp-RSV cpts-530 530/1009 1938 267 N G (val) A (ile) A (ile) A (ile)
6313 218 F A (glu) C (ala) C (ala) C (ala) 7228 523 F C (thr) T
(ile) T (ile) T (ile) 9453 319 L G (cys) A (tyr) A (tyr) A (tyr)
10060 521 L C (phe) C (phe) A (leu) A (leu) 12002 1169 L A (met) A
(met) A (met) G (val) 13565 1690 L C (his) T (tyr) T (tyr) T (tyr)
.sup.1Positive sense
Thus, the ts and attenuation phenotypes of the cpts248 and cpts530
each are associated with a single nucleotide change in the
polymerase gene. The incremental increase in ts and attenuation
phenotypes between the cpts530, and cpts530/1009 or cpts530/1030
was also each associated with a one amino change in L. In these
four examples (i.e., cpts248, cpts530, cpts530/1009, and
cpts530/1030) a single, but different, amino acid substitution in L
conferred the ts and attenuation phenotypes on the progenitor
strains. These amino acid substitutions are acting in cooperation
with the five cpRSV mutations to enhance the stability of the ts
phenotype following replication in animals. The incremental
increase in attenuation and temperature sensitivity observed
between the cpts248 and cpts248/404 was associated with two
nucleotide changes, either or both of which could contribute to the
ts and attenuation phenotypes. The four specific sites in L (i.e.,
those specific for the cpts530, cpts530/1009, cpts530/1030 and
cpts248 viruses) that are singly associated with the ts and
attenuation phenotypes and one or both sites in cpts248/404 are
identified by the findings summarized herein as core regions of the
RSV genome or L protein at which mutation can lead to attenuation.
Although the specific mutations at the four sites in the L protein
were specific amino acid substitutions, it is likely that other
amino acid substitutions as well as in frame insertions or
deletions at these sites and at contiguous amino acids within about
five amino acids of a specific site can also result in
attenuation.
The encoded amino acid changes in L do not appear to involve the
regions of highest sequence conservation among the paramyxovirus
polymerase proteins, the proposed ATP binding site (Stec et al.,
Virology 183:273-287 (1991)), nor the regions suggested to be
homologous to motifs of RNA-dependent RNA and DNA polymerases (Poch
et al., EMBO J. 8:3867-3874 (1989)). It is more likely that the
effect of these mutations is at amino acid level rather than
nucleotide level, given that the mutation does not lie within the
3' and 5' genome termini nor the short gene-start and gene-end
sequences. These RNA regions are thought to contain all of the
cis-acting RNA sequences required for efficient encapsidation,
transcription, replication, and packaging into virions (Collins et
al., Proc. Natl. Acad. Sci. USA 88:9663-9667 (1991); Collins et
al., Proc. Natl. Acad. Sci. USA 93:81-85 (1996), each incorporated
herein by reference).
These results provide the first full-length sequence of a tsRSV
mutant. These results also indicate that pneumoviruses can be
attenuated by the substitution of a single nucleotide that causes
an amino acid change or change in, e.g, a GS sequence. Since the
cpts248 and cpts530 viruses have a high degree of stability of the
ts phenotype both in vitro and in vivo, it is remarkable indeed
that this phenotype was found to be associated with a single,
different amino acid change. Importantly, the cpts248/404,
cpts530/1009, and cpts530/1030 contain at least three mutations
that contribute to the attenuation phenotype, two ts and one non-ts
(e.g., the five cp mutations), and this is a partial non-limiting
explanation for the high level of stability of these viruses in
vitro and in vivo.
Determination of the complete sequence of RSV vaccine virus strains
and of their parental viruses permits analysis at the genetic level
of the stability of vaccine viruses during vaccine virus production
and during shedding by volunteers in clinical trials. The
determination of the genetic basis for the attenuation and ts
phenotypes of the cpts248, cpts530, cpts248/404 cpts530/1009 and
cpts530/1030 viruses provides important new opportunities.
According to the recombinant methods described hereinbelow, it is
readily possible to generate novel vaccine candidates by
site-directed mutagenesis of full-length RSV cDNA from which
infectious viruses can be recovered. For example, it is possible to
add to a cDNA clone of, e.g., the cpts248/404 virus, one or both of
the ts mutations at amino acid position 521 (in the cpts530 mutant)
or 1169 (in the cpts530/1009 mutant) or other attenuating or
stabilizing mutations as desired. In this way, the level of
attenuation of the cpts248/404 virus can be increased in an
incremental fashion and a vaccine strain that has the specific
level of attenuation desired for both safety and immunogenicity can
be generated in a rational way. Similarly, the level of attenuation
of the cpts530/1009 and cpts530/1030 mutants can be increased by
the specific introduction of one or more of the attenuating
mutations in the cpts248/404 virus. These examples of combinatorial
recombinant viruses, incorporating multiple attenuating mutations
from biologically derived mutant strains, overcome many of the
difficulties which attend isolation and production of genetically
stable, satisfactorily attenuated viruses using conventional
approaches. Moreover, the phenotypic stability of these recombinant
cptsRSV mutants can be enhanced by introducing, where possible, two
or more nucleotide substitutions at codons that specify specific
amino acids that are known to confer the attenuation phenotype. In
this way the stability of the attenuation phenotype can be
augmented by site-directed mutagenesis of full-length RSV cDNA.
EXAMPLE VII
Construction of cDNA Encoding RSV Antigenome
A cDNA clone encoding the antigenome of RSV strain A2 was
constructed, as illustrated in FIG. 2. The cDNA was synthesized in
segments by reverse transcription (RT) and polymerase chain
reaction (PCR) using synthetic oligonucleotides as primers and
intracellular RSV mRNA or genome RNA isolated from purified virions
as template. The final cDNA was flanked on the leader end by the
promoter for T7 RNA polymerase, which included three transcribed G
residues for optimal activity; transcription would result in the
donation of these three nonviral G's to the 5' end of the
antigenome. To generate a nearly-correct 3' end, the cDNA trailer
end was constructed to be adjacent to a previously-described
hammerhead ribozyme, which upon cleavage would donate a single
3'-phosphorylated U residue to the 3' end of the encoded RNA
(Grosfeld et al., J. Virol. 69:5677-5686 (1995), incorporated
herein by reference). The ribozyme sequence was followed by a
tandem pair of terminators of T7 RNA polymerase. (The addition of
three 5' G residues and one 31 U residue to a cDNA-encoded RSV
minigenome containing the chloramphenicol acetyl transferase (CAT)
reporter gene had no effect on the expression of CAT when
complemented by RSV.)
FIG. 2 shows the structures of the cDNA and the encoded antigenome
RNA. The diagram of the antigenome (at top) includes the following
features: the 5'-terminal nonviral G triplet contributed by the T7
promoter, the four sequence markers at positions 1099 (which adds
one nt to the length), 1139, 5611, and 7559, the ribozyme and
tandem T7 terminators, and the single nonviral 3'-phosphorylated U
residue contributed to the 3' end by ribozyme cleavage (the site of
cleavage is indicated with an arrow).
Cloned cDNA segments (FIG. 2, middle) representing in aggregate the
complete antigenome were constructed by RT-PCR of RSV mRNA or
genome RNA. The complete antigenome cDNA is called D46 or D53; the
different names referring to different preparations of the same
plasmid. cDNAs containing the lefthand end of the antigenome,
spanning from the T7 promoter and leader region complement to the
SH gene and called D13, were assembled in a version of pBR322 (FIG.
2, bottom) in which the naturally-occurring BamHI site had been
ablated by mutagenesis and the PstI-EcoRI fragment replaced with a
synthetic polylinker containing unique restriction sites (including
BstBI, BstXI, PacI, BamHI, MluI) designed to facilitate assembly.
The box in FIG. 2 shows the removal of the BamHI site. The
naturally occurring BamHI-SalI fragment (the BamHI site is shown in
the top line in positive sense, underlined) was replaced with a
PCR-generated BglII-SalI fragment (the BglII site is shown in the
bottom line, underlined; its 4-nt sticky end [italics] is
compatible with that of BamHI). This resulted in a single nt change
(middle line, underlined) which was silent at the amino acid level.
These modifications to the vector facilitated construction of the
cDNA by rendering unique a BamHI site in the antigenome cDNA.
The G, F and M2 genes were assembled in a separate plasmid, as were
the L, trailer and flanking ribozyme and tandem T7 transcription
terminators. The G-to-M2 piece was then inserted into the
PacI-BamHI window of the leader-to-SH plasmid. This in turn was the
recipient for the L-trailer-ribozyme-terminator piece inserted into
the BamHI to MluI window, yielding the complete antigenome.
Four restriction site markers (FIG. 3) were introduced into the
antigenome cDNA during the original construction by incorporating
the changes into oligonucleotide primers used in RT-PCR. This was
done to facilitate assembly, provide a means to identify
recombinant virus, and illustrate the ability to introduce changes
into infectious RSV. Three sites were in intergenic regions and the
fourth in a nontranslated gene region, and they involved a total of
five nt substitutions and a single nt insertion. This increased the
length of the encoded antigenome by one nt from that of wild-type
to a total of 15,223 nt (SEQ ID NO:1, which depicts the 5' to 3'
positive-sense sequence of D46, whereas the genome itself is
negative-sense; note that position four can be either G or C).
The sequence markers were inserted into the cDNA-encoded antigenome
RNA as shown in FIG. 3. Sequences are positive sense and numbered
relative to the first nt of the leader region complement as 1;
identities between strains A2 and 18537 (Johnson and Collins, J.
Gen Virol. 69:2901-2906 (1988), incorporated herein by reference),
representing subgroups A and B, respectively, are indicated with
dots; sequences representing restriction sites in the cDNA are
underlined; GS and GE transcription signals are boxed; the
initiation codon of the N translational open reading frame at
position 1141 is italicized, and the sequence markers are shown
underneath each sequence. In the top sequence, a single C residue
was inserted at position 1099 to create an AflII site in the NS2-N
intergenic region, and the AG at positions 1139 and 1140
immediately upstream of the N translational open reading frame were
replaced with CC to create a new NcoI site. In the middle sequence,
substitution of G and U at positions 5612 and 5616, respectively,
created a new StuI site in the G-F intergenic region. And, in the
bottom sequence of FIG. 3, a C replacement at position 7560 created
a new SphI site in the F-M2 intergenic region.
All cDNAs were sequenced in their entirety, in most instances from
several independent cDNAs, prior to assembly. The plasmids encoding
individual RSV proteins are described in Grosfeld et al., J. Virol.
69:5677-5686 (1995) and Collins et al., supra, (1995), each of
which is incorporated herein by reference. The complete cDNA was
also sequenced in its entirety following assembly.
EXAMPLE VIII
Transfection and Recovery of Recombinant RSV
The method of the invention for producing infectious RSV from
cDNA-expressed antigenome involves its coexpression with those RSV
proteins which are sufficient to (i) produce an antigenome
nucleocapsid capable of RNA replication, and (ii) render the
progeny genome nucleocapsid competent for both RNA replication and
transcription. Transcription by the genome nucleocapsid provides
all of the other RSV proteins and initiates a productive
infection.
Plasmid-borne cDNA encoding the antigenome was transfected,
together with plasmids encoding proteins N, P, L and M2(ORF1), into
HEp-2 cells which had been infected with a recently-described
vaccinia virus MVA strain recombinant which expresses the T7 RNA
polymerase (Wyatt et al., Virol. 210:202-205 (1995), incorporated
herein by reference). The MVA strain is a host range mutant which
grows permissively in avian cells whereas in mammalian cells there
is a block at a late stage in virion maturation that greatly
reduces the production of infectious virus. In HEp-2 cells, the MVA
recombinant was similar to the more commonly-used WR-based
recombinant (Fuerst et al., Proc. Natl. Acad. Sci. USA 83:
8122-8126 (1986)) with regard to the level of expression of T7
polymerase and cytopathogenicity, but the level of progeny produced
was sufficiently low that supernatants could be passaged to fresh
cells with minimal cytopathogenicity. This should facilitate the
recovery of any recombinant RSV which might be produced in
transfected, vaccinia virus-infected cells.
Transfection and recovery of recombinant RSV was performed as
follows. Monolayer cultures of HEp-2 cells received, per single
well of a six-well dish, one ml of infection-transfection medium
prepared by mixing five plasmids in a final volume of 0.1 ml
Opti-MEM (Life Technologies) medium, namely 0.4 .mu.g each of
antigenome, N and P plasmids, and 0.1 .mu.g each of L and M2(ORF1)
plasmids. This was combined with 0.1 ml of Opti-MEM containing 12
.mu.l LipofectACE (Life Technologies). After 15 min incubation at
room temperature, this was combined with 0.8 ml of OptiMEM
containing 2% heat-inactivated fetal bovine serum and
1.5.times.10.sup.6 pfu of strain MVA vaccinia virus recombinant
encoding T7 RNA polymerase (Wyatt et al., supra). This was added to
the cells and replaced one day later by Opti-MEM containing 2%
serum. Cultures were incubated at 32.degree. C. and harvested on
day three. Incubation at 32.degree. C. was used because it was
found that the MVA virus is slightly temperature sensitive and is
much more efficient at this lower temperature.
Three days post-transfection clarified culture supernatants were
passaged onto fresh HEp-2 cells and overlaid with methyl cellulose
(for subsequent antibody staining) or agarose (for plaque
isolation). After incubation for five days under methyl cellulose,
the cells were fixed and stained by an indirect horseradish
peroxidase method using a mixture of three murine monoclonal
antibodies to the RSV F protein followed by an anti-mouse antibody
linked to horseradish peroxidase, following the general procedure
of Murphy et al., Vaccine 8:497-502 (1990).
Numerous RSV-like plaques were detected against a background of
cytopathogenicity that presumably was due to a low level of MVA-T7
recombinant virus. The plaques contained an abundant amount of the
RSV F protein, as indicated by brown-black coloration, and
displayed cytopathic effects characteristic of RSV, notably
syncytium formation.
The RSV-like plaques were picked from plates which were incubated
under agarose and stained with neutral red. They were propagated
and compared to a laboratory strain of RSV strain A2 by plaque
assay and antibody staining. The plaques derived from the
transfected cultures closely resembled those of the laboratory
strain. One difference was that the plaques derived from the
transfected cultures appeared to be slightly smaller than those
from the laboratory strain, with centers which were less well
cleared. The recombinant virus may differ phenotypically from this
particular wild-type isolate, possibly being slightly more
restricted in cell-to-cell spread and exhibiting a reduced rate of
cell killing. With regard to the propagation of released virus, the
yields of the recombinant versus laboratory virus in HEp-2 cells
were essentially identical at 320 or 37.degree. C. In preliminary
studies, the recombinant and laboratory viruses were
indistinguishable with regard to the accumulation of intracellular
RSV mRNAs and proteins.
Plaque-purified, thrice-passaged recombinant RSV was analyzed in
parallel with laboratory virus by RT-PCR using three primer pairs
flanking the four inserted markers. Three independent
plaque-purified recombinant RSV isolates were propagated in
parallel with an uninfected control culture. Clarified medium
supernatants were treated with polyethylene glycol and high salt
(Zoller and Smith, DNA 3:479-488 (1984)) to precipitate virus and
RNA was extracted from the pellets with Trizol.TM. (Life
Technologies). These RNAs, in parallel with additional controls of
no added RNA or 0.1 .mu.g of RNA from a laboratory isolate of
strain A2, were treated with DNAse, repurified, annealed each with
50 ng of random hexamers and incubated under standard RT conditions
(40 .mu.l reactions) with or without reverse transcriptase (Connors
et al., Virol. 208:478-484 (1995), incorporated herein by
reference). Aliquots of each reaction were subjected to PCR (35
cycles of 94.degree. C. for 45s, 37.degree. C. for 30s, 72.degree.
C. for 1 min) using three different pairs of synthetic
deoxyoligonucleotide primers. Primer pair (A): positive-sense,
positions 925-942 and negative-sense, positions 1421-1440, yielding
a predicted product of 516 bp (517 bp in the case of the
recombinant viruses) that included the AflII and NcoI sites
inserted at, respectively, the junction of the NS2 and N genes and
in the N gene. Primer pair (B): positive-sense, positions 5412-5429
and negative-sense, 5930-5949, yielding a predicted product of 538
bp spanning the StuI site inserted at the junction between the G
and F genes. Primer pair (C): positive-sense, 7280-7297 and
negative-sense, 7690-7707, yielding a 428 bp fragment spanning the
SphI site inserted at the junction between the F and M2 genes. PCR
products were analyzed by electrophoresis on neutral gels
containing 1% agarose and 2% low-melting agarose in parallel with
HaeIII-digested X174 DNA molecular length markers and visualized by
staining with ethidium bromide. PCR products of the expected sizes
were produced. The production of each was dependent on the RT step,
indicating that each was derived from RNA rather than contaminating
cDNA.
PCR products were analyzed by digestion with restriction enzymes.
Digestion of products of primer pair A with AflII or NcoI yielded
fragments corresponding to the predicted 177 and 340 bp (AflII) or
217 and 300 bp (NcoI). Digestion of products of primer pair B with
StuI yielded fragments comparable to the predicted 201 and 337 bp.
Digestion of products from reactions with primer pair C with SphI
yielded products corresponding to the predicted 147 and 281 bp. The
digests were analyzed by gel electrophoresis as above. The presence
of residual undigested PCR product with AflII was due to incomplete
digestion, as was confirmed by redigestion. Thus, the restriction
enzyme digestion showed that the PCR products representing
recombinant virus contained the expected restriction site markers
while those representing the laboratory strain did not. Nucleotide
sequence analysis of cloned PCR product confirmed the sequences
spanning the restriction site markers.
As shown in Table 38, the efficiency of RSV production when
complemented by N, P, L and M2(ORF1) was relatively high, ranging
in three experiments from an average of 9.9 to 94.8 plaques per 0.4
.mu.g of input antigenome cDNA and 1.5.times.10.sup.6 cells. Since
these plaques were derived from liquid overlay, the number of
infected cells present in each well of the original transfection
was not known. Nearly every transfected well (54 of 56 in Table 38)
produced virus. Since the yield of released RSV per infected cell
typically is very low (.about.10 pfu) even under ideal conditions,
and since many wells yielded many times this amount (up to 169
plaques), it is likely that several RSV producing cells were
present in many of the wells of transfected cells.
RSV was not recovered if any of the plasmids were omitted, as shown
in Table 38. The requirement for M2(ORF1) also could be satisfied
with the complete gene, M2(ORF1+2), provided the level of its input
cDNA was low (0.016 .mu.g per 1.5.times.10.sup.6 cells (Table 38).
At higher levels, the production of virus was greatly reduced,
suggesting that an inhibition of minigenome RNA synthesis
associated with M2(ORF2) also operates on the complete genome
during productive infection.
These results showed that the production of infectious RSV was
highly dependent on expression of the M2(ORF1) protein in addition
to N, P and L. Furthermore, it showed that the optimal method of
expression of M2(ORF1) was from an engineered cDNA in which ORF2
had been deleted, although the complete cDNA containing both ORFs
also supported the production of RSV.
Thus, the present invention demonstrates that transcription by RSV
differs from that of from previously-described nonsegmented
negative strand RNA viruses in requiring a fourth protein
designated here as M2(ORF1), and previously called 22K or M2
(Collins et al., J. Virol. 54:65-71 (1985)). The M2(ORF1) protein
was found to be an RNA polymerase elongation factor that is
important for processive, sequential transcription, and therefore
must be provided (e.g., endoded by the genome or antigenome or
expressed in trans by a separate plasmid or sequence within a
shared vector). (see, e.g., Collins et al., Proc. Natl. Acad. Sci.
USA 93:81-85 (1996)). This requirement provides the capability, as
part of this invention, for introducing specific, predetermined
changes into infectious RSV.
TABLE-US-00038 TABLE 38 Production of infectious RSV was dependent
on expression of M2 ORF 1. Complementing plasmids (.mu.g cDNA per
1.5 .times. 10.sup.6 Production of infectious RSV cells and
antigenome #plaques .times. # wells* cDNA) 0.4 .mu.g expt. 1 expt.
2 expt. 3 N(0.4) P(0.4) 0 .times. 24 0 .times. 12 0 .times. 12
L(0.1) N(0.4) 0 .times. 19.sup..sctn. 0 .times. 4 9 .times. 1
P(0.4) 1 .times. 2 3 .times. 1 10 .times. 1 L(0.1) 2 .times. 2 5
.times. 1 14 .times. 2 M2 [ORF1 + 2] (0.016) 3 .times. 1 6 .times.
1 22 .times. 1 9 .times. 1 28 .times. 1 av. 0.38 10 .times. 1 32
.times. 1 13 .times. 1 49 .times. 1 34 .times. 1 70 .times. 2 51
.times. 1 166 .times. 1 169 .times. 1 av. 10.9 av. 48.6 N(0.4) 0
.times. 1 11 .times. 1 0 .times. 1 55 .times. 1 P(0.4) 1 .times. 1
12 .times. 1 2 .times. 1 59 .times. 1 L(0.1) 2 .times. 2 13 .times.
1 4 .times. 1 65 .times. 1 M2 [ORF1] (0.1) 3 .times. 2 21 .times. 1
5 .times. 1 71 .times. 1 4 .times. 1 24 .times. 1 8 .times. 2 72
.times. 1 5 .times. 2 26 .times. 1 10 .times. 3 87 .times. 1 6
.times. 4 30 .times. 2 19 .times. 1 97 .times. 1 7 .times. 2 33
.times. 2 20 .times. 1 100 .times. 1 9 .times. 1 42 .times. 1 23
.times. 1 109 .times. 1 10 .times. 2 73 .times. 1 128 .times. 1 av.
9.9 147 .times. 1 av. 13.7 148 .times. 1 av. 94.8 *Supernatants
from transfected cultures (10.sup.6 cells per well) were passaged
onto fresh HEp-2 cells, overlaid with methyl cellulose, and stained
with F-specific monoclonal antibodies. .sup..sctn.Read as follows:
19 wells had 0 plaques, 2 wells had 1 plaque each, 2 wells had 2
plaques each, and 1 well had 3 plaques.
EXAMPLE IX
Construction of an Infectious Recombinant RSV Modified to
Incorporate Phenotype-Specific Mutations of RSV Strain cpts530
This Example illustrates the introduction of specific predetermined
mutations into infectious RSV using the recombinant methods
described herein. As noted above, the complete nucleotide sequence
of cpts530 RSV was determined and 5 mutations known to be present
in the parent cpRSV were retained in cpts530, the further
attenuated derivative. One additional nucleotide change was
identified at nucleotide (nt) position 10060, which resulted in a
phenylalanine to leucine change at amino acid position 521 in the
large polymerase (L) protein (see Tables 37, 39). This single amino
acid substitution was introduced alone or in combination with the
cp mutations into the full-length cDNA clone of wild-type A2 RSV.
Analysis of infectious viruses recovered from mutant cDNAs
indicated that this single mutation specified complete restriction
of plaque formation of recombinant cp530 in HEp-2 cell monolayer
cultures at 40.degree. C., and the level of temperature sensitivity
was not influenced by the presence of the 5 cpRSV mutations. These
findings identify the phenylalanine to leucine change at amino acid
position 521 in the L protein as the mutation that specifies the ts
phenotype of cpts530. Similarly, one additional nucleotide change
was identified in the cpts530/1009 recombinant in comparison to its
cpts530 parent virus (Table 37). This nucleotide substitution at
position 12002 resulted in an amino acid change in L at position
1169 at which a methionine in the wild-type virus was replaced by a
valine in the cpts530/1009 mutant. This mutation has also been
introduced into recombinant RSV, and the recovered virus was
temperature sensitive. These findings identify the methionine to
valine change at position 1169 as the mutation that specifies the
greater level of temperature sensitivity of cpts530/1009 over that
of cpts530.
The levels of temperature sensitivity among the 530, 530/1009 and
530/1030 recombinant virus have been confirmed with RSV-CAT or
RSV-Luciferase minigenome (see above) monitored by enzyme assay or
Northern blot analysis. For example, at the elevated temperature of
37.degree. C., the luciferase activity generated by selected
mutants relative to wild-type L protein was 18.4%, 1.5% and 0.4%
for 1009, 530, and the double mutant pTM1-L support plasmid. These
exemplary mutations also decreased L function at 32.degree. C. with
70% activity for 1009, 40% activity for 530, and 12.5% activity for
530/1009 L protein compared to wt L protein. The effects of these
mutations on transcription and replication can also be determined
using the minigenome system, alone or in combination with the
recombinant viral methods disclosed herein.
TABLE-US-00039 TABLE 39 Mutations introduced into the RSV
full-length CDNA clone. Sequence Sequence of Restriction Amino Acid
Mutation of wt Mutation Site Change site [L].sup.1 .sub.
9398CTTAAGA .sub. 9398 Bsu36I -- site [L] .sub.11846TACATA
.sub.11846 SnaBI -- site [L] .sub.13339GTCTTAAT .sub.13339 PmeI --
site [L] .sub.14082CGTACAG .sub.14082 RsiII -- site [L]
.sub.14318TGTAACA .sub.14318 BsiEI -- site [L] .sub.14475TATGTA
.sub.14475 SnaBI -- HEX [F] .sub. 5848AATATCAAGAAA .sub. 5848
AAGG*AA SspI .sub. 65lys.fwdarw.glu HEX [F] .sub. 5958AGCAGAGAA
.sub. 5958 GG*A ScaI .sub. 101gln.fwdarw.pro cp [F] .sub.
1935ATCAGTT .sub. 1935 * T ClaI .sub. 287val.fwdarw.ile cp [F]
.sub. 6311TAGAAA .sub. 6311 NruI .sub. 213glu.fwdarw.ala cp [F]
.sub. 7228ACAAAT .sub. 7228 AseI .sub. 522thr.fwdarw.ile cp [L]
.sub. 9453T .sub. 9453TAGATAC lose AccI .sub. 319cys.fwdarw.tyr cp
[L] .sub.13555TATTAACTAAAGAT .sub.13555T TAAATAC HpaI
.sub.1690his.fwdarw.tyr 248 [L] .sub.10982TCATGCTCAA .sub.10982
TGT*G SphI .sub. 851gln.fwdarw.leu 404 [M2] .sub. 7606TATGTCACGA
.sub. 7606C*ATG NruI -- 404 [L] .sub.12042TTGGAT .sub.12042 HhoI
.sub.1153asp.fwdarw.glu 530 [L] .sub.10059TTC .sub.10059TTA* --
.sub. 521phe.fwdarw.leu 1009 [L] .sub.11992CCACTGAGATGATG
.sub.11992 TC BsfXI .sub.1169met.fwdarw.val 1030 [L] .sub.12452 TAT
.sub.12452GCTAACAA*AT lose HpaI .sub.1321tyr.fwdarw.asn Note:
Nucleotide differences between wild-type and mutants [at the
corresponding positions of are underlined. Recognition sites of
restriction endonucleases are in italics. Codons in which the
introduced nucteotide change[s] results in amino acid substitution
are in bold. Asterisk identifies the single nucleotide change that
was present in the biologically-derived mutant virus. Numbering
system reflects the one nucleotide insertion in the full length
cDNA. .sup.1indicates the gene into which the mutation was
introduced.
To incorporate the cpts530 and the cpts1009 specific mutations into
a defined, attenuated recombinant RSV vaccine virus, the cDNA-based
recovery system described herein was employed as follows. The
previously-described RSV A2 wild-type full-length cDNA clone
(Collins et al., supra., (1995)) was designed in the original
construction to contain a single nucleotide insertion of C in the
cDNA clone at nt position 1099 (which creates an AflII site) and a
total of 6 additional nucleotide substitutions at 4 loci. Thus, the
nucleotide numbering system for the naturally occurring virus and
for the recombinant viruses derived from cDNA are out of register
by one nt after position 1099. The nucleotide numbering in Tables
36 and 37, above, represents the positions for the naturally
occurring viruses, while those for the cDNA clones (Table 39) and
recombinant viruses derived from cDNA clones are one nucleotide
more. One of the 6 nucleotide substitutions is a G to C change in
genome sense at nt position 4 in the leader sequence. This
nucleotide variation has been detected in non-recombinant RSV and
was not found to have an effect on the temperature sensitivity of
virus replication in tissue culture or in mice (Firestone, et al.,
Virology, 225:419-522 (1996), incorporated herein by reference).
Table 39 lists the various mutations which were inserted into the
RSV cDNA in this and subsequent Examples.
Intermediate clones (D50 and D39) were used to assemble the
full-length RSV cDNA clone D53, which encodes positive-sense RSV
antigenome (FIG. 4). The D50 plasmid contains the RSV genome from
the leader to the M2-L overlap downstream of a T7 promoter, while
the D39 plasmid encodes the full-length L gene and the trailer
followed by the hammerhead ribozyme and two T7 terminators
(approximately 7 kb in length) bordered by BamHI and MluI
restriction sites. The full-length RSV cDNA clone (D53) used in
transfections to rescue infectious virus was assembled by inserting
the BamHI-MluI fragment of the D39 plasmid into the D50 plasmid
(see U.S. patent application Ser. No. 08/720,132; and published PCT
Application No. PCT/US96/15524, each incorporated herein by
reference). D50 was further separated into several pieces each
placed in a phagemid plasmid for the purposes of facilitating
mutagenesis: one piece was an Xbal-EcoRI fragment containing the N
gene (cDNA pUC118.D50N), and one was a StuI-BamHI fragment
containing the F and M2 genes (pUC118.F-M2). D39 was further
separated into two pieces each placed in a separate phagemid
plasmid: one piece (left hand half, cDNA pUC119.L1) runs from the
BamHl site to the PmlI site at nucleotide 12255 (note that the
sequence positions assigned to restriction site locations here and
throughout are intended as a descriptive guide and do not alone
precisely define all of the nucleotides involved), and the other
(right hand half, cDNA pUC119.L2) from the Pm/I site to the end of
the T7 terminator.
Mutations were placed into the pUC118- and pUC119-based constructs
illustrated in the bottom row of FIG. 4 following standard
procedures (see, e.g., Kunkel et al., Methods Enzymol, 54:367-382
(1987), incorporated herein by reference). The plasmids were
propagated in a dut ung strain of E. coli., in this case CJ236, and
single stranded DNA was prepared by infection with a helper phage,
in this case M13KO7. Phosphorylated synthetic oligonucleotides each
containing one or more nucleotide changes of interest were
prepared, annealed to the single stranded template singly or in
combination, and used to direct DNA synthesis by T4 DNA polymerase.
The products were ligated and transformed into a non-dut ung strain
of E. coli, in this case DH5alpha or DH10B. Miniprep DNA of the
transformant colonies was screened for the presence of the mutation
by restriction enzyme digestion or by nucleotide sequence analysis
of the mutagenized region. Fragments containing the appropriate
mutations were transferred from the pUC constructs back into the
D50 or D39 plasmids, which in turn were assembled into a
full-length clone designated D53. Recombinant virus was recovered
in HEp-2 cells by complementing the D53 plasmid with a mixture of
the four support plasmids encoding the N, P, L and M2 (ORF1)
proteins, as described above.
Four types of mutations are involved in this and subsequent
examples describing specific recombinant RSV incorporating
biologically derived mutations (see Tables 36, 37, 39):
(1) The first group of mutations involves six translationally
silent new restriction site markers introduced into the L gene,
collectively called the "sites" mutations. The six sites are
Bsu36I, SnaBI, PmeI, RsrII, BstEII and a second, downstream SnaBI
site, and are underlined in FIG. 4 above the D53 diagram. These six
changes, collectively referred to as the "sites" mutations, were
inserted for the purpose of facilitating cDNA construction. Also,
it is known that recombination can occur during transfection
between the D53 plasmid and the support plasmids, i.e., the N, P,
M2(ORF1) and L plasmids (Garcin et al., EMBO J. 14:6087-6094
(1995), incorporated herein by reference. These restriction sites
in L are present in the D53 construct but not in the L support
plasmid, and thus provide a marker to confirm that recombination in
L did not occur. This is particularly important since many of the
attenuating mutations occur in L.
(2) The second group of mutations involves two amino acid changes
in the F gene (FIG. 4, Table 39). The cpRSV, and hence all of its
derivatives, is derived from a wild-type virus called HEK-7. The
sequence of the original D53 cDNA differs from that of HEK-7 by
single nucleotide substitutions at seven positions. One is at
nucleotide 4, which is a C (in negative sense) in the original D53
and G in the HEK virus. However, biologically-derived viruses have
been shown to contain either assignment, and can fluctuate between
the two, and so this difference is considered incidental and not
considered further here. Four other nucleotide substitutions were
silent at the amino acid level; these were two changes in F, at
positions 6222 and 6387, one in the F-M2 intergenic region at
position 7560, and one in L at position 10515). These also are not
considered significant and are not considered further. Finally,
there were two nucleotide substitutions, each in the F gene, which
each resulted in an amino acid substitution (Table 39). These two
changes, collectively called the "HEK" assignments, were introduced
into D53 such that the encoded recombinant wild-type virus would be
identical at the amino acid level to the HEK-7 wild-type parent of
the biologically-derived cpts mutants. Note that each of these
changes was designed to also introduce a new restriction enzyme
recognition site for the purpose of monitoring the presence of the
introduced mutation in cDNA as well as in recovered virus.
(3) The third group of mutations involved the five amino acid
substitutions found in the cpRSV virus, collectively called the
"cp" mutations. These are present in all of the
biologically-derived cpts viruses and contribute to the attenuation
phenotype. In biologically-derived cpRSV, each of these amino acid
changes is due to a single nucleotide change. As shown in Table 39,
when the amino acid coding change was introduced into cDNA to make
recombinant virus in four of the five cases each coding change was
made to involve two nucleotide substitutions, which renders the
recombinant RSV highly resistant to reversion to wild-type. Note
that four of these changes were designed to introduce a new
restriction enzyme site, whereas the fifth was designed to ablate
an existing site, thus providing a method for monitoring the
presence of the mutation by the presence or absence of the
restriction site in cDNA or RT-PCR products generated from
recombinant viruses.
(4) The fourth group of mutations involves point mutations specific
to individual, biologically derived cpts viruses (Table 39, FIG.
4), which are named after the biological step at which they were
acquired. For example, derivation of the cpts248/404 virus from
cpRSV in the following Example involved two steps of mutagenesis.
The first yielded the cpts248 virus, which sustained a single amino
acid change that is therefore called the 248 mutation. The second
mutagenesis step, applied to cpts248, yielded the cpts248/404
virus, which contains an amino acid change in L called the 404(L)
mutation and a nucleotide change in the gene start (GS) signal of
M2, called 404(M2) mutation. The remaining mutations, namely 530,
1009 and 1030, each involve a single (different) amino acid change.
The 404(M2) mutation is noteworthy because it involves the GS
transcription signal (and does not involve a protein-coding
sequence) and because this mutation was shown in a minigenome
system to be important for synthesis of the mRNA. Kuo et al., J.
Virol. 71:4944-4953 (1977) (incorporated herein by reference). As
outlined in Tables 36, 37, and 39, the amino acid coding changes of
the 248, 404(L), and 1009 mutations were inserted into recombinant
virus using two nucleotide substitutions for the purpose of
improved genetic stability. Also, the 248, 404(M2), 404(L), and
1009 mutations for recombinant virus were each designed to
introduce a new restriction site for monitoring purposes, while the
1030 mutation was designed to ablate an existing site.
In the present Example, several pUC118- and pUC119-based constructs
were derived from the D50 and D39 plasmids and desired mutations
were introduced into these constructs (FIGS. 4, 5). Fragments
containing the appropriate mutations were transferred from the pUC
constructs back into the D50 or D39 plasmids as indicated, which in
turn were assembled into a full-length clone. In this way, six
different types of D53 full-length derivative clones were generated
(FIGS. 4, 5). In FIG. 5, the D53 constructs lacked the two HEK
mutations in F (see FIG. 4).
Mutagenesis was performed using the Muta-Gene.RTM. Phagemid in
vitro Mutagenesis kit (Bio-Rad, Hercules, Calif.) as recommended by
the manufacturer. The mutagenized constructs were transformed into
competent E. coli DH10B (Life Technologies). Miniprep DNA of the
transformant colonies was screened for the presence of the mutation
by restriction enzyme digestion (see below) or by nucleotide
sequence analysis of the mutagenized region.
The six translationally silent restriction site markers, the 530
mutation (.sub.521phe.fwdarw.leu), and the 5 cp mutations (Table
39) were introduced into the pUC-based constructs and subcloned
into the D50 and D39 plasmids as indicated in FIGS. 4 and 5. The
various full-length cDNA constructs were assembled using D50 and
D39 constructs containing different combinations of the above
mentioned mutations.
In the final cDNA constructs, the presence of the 530 and the cp
mutations were confirmed by sequence analysis, while the presence
of the silent restriction sites were determined by restriction
endonuclease analysis. Each D53-based construct was analyzed using
various restriction enzymes (e.g. HpaI, AccI, HindIII, PstI), and
the restriction patterns of the newly generated full-length cDNA
clones were compared with that of the previously rescued wild-type
full-length cDNA clone. This restriction analysis was used to
determine if an insertion or deletion of 100 nt or more had
occurred during the bacterial amplification of the full-length
plasmids.
Transfection was performed as described previously (Collins, et
al., Proc. Natl. Acad. Sci. USA, 92:11563-11567 (1995),
incorporated herein by reference). Briefly, monolayers of HEp-2
cells were infected at an MOI of 1 with recombinant vaccinia virus
MVA strain expressing T7 RNA polymerase (MVA-T7) and were
transfected using LipofectACE (Life Technologies) with a D53
antigenomic construct plus the N, P, L and M2 (ORF1) pTM1 support
plasmids. On day three, supernatants (clarified medium) were
passaged onto fresh HEp-2 cells for amplification of rescued virus.
Virus suspensions from this first amplification were harvested 5
days after infection and, following inoculation at various
dilutions onto monolayers of HEp-2 cells, were overlayed with
methylcellulose for plaque enumeration or with agarose for plaque
harvest and biological cloning. Plaque enumeration was performed
using a monoclonal antibody-horseradish peroxidase staining
procedure as previously described (Murphy et al., Vaccine,
8:497-502 (1990), incorporated herein by reference). The recovered
recombinant viruses were biologically cloned by three successive
plaque purifications, and then used to generate virus suspensions
following two passages on HEp-2 cells. The biological cloning was
important to ensure a homogeneous population of the recovered
viruses, as recombination may arise during the first step of the
rescue between the plasmid representing the full-length cDNA of RSV
and the support plasmids containing RSV genes (Garcin et al., EMBO
J., 14:6087-6094 (1995), incorporated herein by reference). These
biologically cloned and amplified virus suspensions were used in
further molecular genetic or phenotypic characterization of the
recombinant viruses. Two biologically cloned recombinant viruses
were generated for each of the cDNA constructs (FIG. 5) except for
cp.sub.L530-sites and cp530-sites, for which only one biological
clone was generated. In each case, when there were sister clones,
they were indistinguishable on the basis of genetic and biological
analyses described below. A representative example of the foregoing
constructs corresponding to D53-530-sites (alternatively designated
A2 ts530-s cl1cp, or ts530-sites) has been deposited under the
terms of the Budapest Treaty with the ATCC and granted the
accession number VR-2545.
The recombinant RSVs generated as described above were genetically
characterized to determine if they indeed contained each of the
introduced mutations. Monolayers of HEp-2 cells were infected with
biologically cloned recombinant virus and total RNA was harvested 4
to 5 days post infection as described above. RT was performed using
random hexamer primers and the generated cDNA was used as template
in PCR using the Advantage.TM. cDNA PCR Kit (Clontech Lab. Inc.,
Palo Alto, Calif.) to generate three fragments representing almost
the full-length of the recombinant RSV genomes. The PCR fragments
corresponded to the RSV genome between nt positions 1-5131,
5949-10751 and 8501-15179. Also, a 544 bp fragment representing a
portion of the L gene in the region of the 530 mutation between nt
positions 9665 and 10209 was generated. This short PCR fragment was
used in cycle sequencing (using 71001 delta TAQ.TM.* Cycle
Sequencing Kit, USB, Cleveland, Ohio) to confirm the presence or
the absence of the 530 mutation in the recovered recombinant virus,
whereas the large PCR products were used in restriction enzyme
digestion to confirm the presence of the silent restriction site
markers and the cp mutations which were marked with specific
restriction sites.
To verify that the recombinant RSVs produced according to the above
methods incorporated the desired phenotype, i.e., the phenotype
specified by the incorporated sequence change(s), the efficiency of
plaque formation (EOP) of the recombinant RSVs and the
nonrecombinant control viruses was determined. Specifically, plaque
titration at 32, 37, 38, 39 and 40.degree. C. using HEp-2 monolayer
cultures in temperature controlled water baths was conducted, as
described previously (Crowe et al., Vaccine, 11:1395-1404 (1993);
Firestone, et al., Virology 225:419-522 (1996), each incorporated
herein by reference). Plaque identification and enumeration was
performed using antibody staining as indicated above.
The level of temperature-sensitivity of the recombinant viruses and
the wild-type and biologically derived mutant cpts530 viruses is
presented in Table 40. These data show that the introduction of the
silent restriction sites or the cp mutations does not confer a ts
phenotype. This latter observation is consistent with our previous
finding that the cpRSV is a ts.sup.+ virus (Crowe, et al., Vaccine,
12:691-699 (1994)).
TABLE-US-00040 TABLE 40 Comparison of the Efficiency of Plaque
Formation.sup.a of Recombinant and Biologically Derived Viruses in
HEp-2 Cells at Various Temperatures. Reduction in Virus titer
(log.sub.10) at RSV Titer (log.sub.10pfu/ml indicated temperature
at indicated temp.).sup.b compared to that at 32.degree. C. Virus
32 38 39 40 39 40 Wild-type.sup.c 5.7 5.5 5.4 5.3 0.3 0.4 r-sites
5.4 5.1 5.2 5.2 0.2 0.2 rcp-sites 6.1 5.7 5.7 5.7 0.4 0.4 r530 6.3
6.0 4.4 <0.7 1.9 >5.6 r530-sites 6.4 6.1 4.4 <0.7 2.0
>5.7 rcp.sub.L530-sites 5.8 5.9 3.8 <0.7 2.0 >5.1
rcp530-sites 6.3 5.0 4.1 <0.7 2.2 >5.6 cpts530.sup.c 6.6 5.8
4.4 <0.7 2.2 >5.9 .sup.aEfficiency of plaque formation of the
various RSV strains was determined by plaque titration on
monolayers of HEp-2 cells under semisolid overlay for five days at
the indicated temperatures (.degree. C.). .sup.bVirus titers are
the average of two tests, except for r-sites and r cp-sites where
data were derived from a single test. .sup.cBiologically derived
control viruses.
The above findings confirm that ts phenotype of the biologically
derived cpts530 virus is specified by the single mutation
identified above as being unique to this attenuated RSV strain.
Genetic analysis of the cpts530 strain was confirmed in this
context by the introduction of the 530 mutation into a full-length
cDNA clone of the A2 wild-type ts.sup.+ parent virus, followed by
the recovery of a ts recombinant virus bearing the 530 mutation.
Analysis of the level of temperature sensitivity of this and
additional recombinant viruses containing the 530 and cp mutations
revealed that the level of temperature sensitivity specified by the
530 mutation was not influenced by the five cp mutations. Thus, the
methods and compositions of the invention identified the 530
mutation as the ts phenotype-specific mutation which is attributed
with further attenuation of the cpts530 virus in model hosts over
that of its cpRSV parent (Crowe et al., Vaccine, 12:783-90 (1994),
Crowe et al., Vaccine, 13:847-855 (1995), each incorporated herein
by reference).
In addition to the above findings, introduction of the 1009
mutation or 1030 mutation into recombinant RSV, in combination with
the cpts530 mutation, generated recombinants whose levels of
temperature sensitivity were the same as those of the respective,
biologically derived cpts530/1009 and cpts530/1030 RSV mutants.
The above findings illustrate several important advantages of the
recombinant methods and RSV clones of the invention for developing
live attenuated RSV vaccines. The insertion of a selected mutation
into recombinant RSV, as well as the recovery of mutations from the
RSV A2 cDNA clone were relatively efficient. The antigenome cDNA
clone used in this example had been modified in the original
construction to contain changes at five different loci, involving 6
nucleotide substitutions and one nucleotide insertion. Mutagenized
virus are also described containing mutations at an additional
twelve loci involving 24 additional nucleotide substitutions. The
fact that only the 530 mutation imparted a phenotype detectable in
tissue culture indicates the relative ease of manipulation of this
large RNA genome. Although recombination between the support
plasmids and the full-length clone that is mediated by the vaccinia
virus enzymes can occur (Garcin et al., EMBO J., 14:6087-6094
(1995)), its frequency is sufficiently low that each of the 10
viruses analyzed here possessed the mutations present in the cDNA
clone from which it was derived. Thus, it is readily feasible to
introduce further attenuating mutations in a sequential manner into
RSV, to achieve a desired level of attenuation.
The demonstrated use of the present RSV recovery system for direct
identification of attenuating mutations and the established success
for manipulating recombinant RSV allow for identification and
incorporation of other desired mutations into live infectious RSV
clones. Previous findings from clinical studies and sequence
analysis of the cpRSV virus suggest that the set of five non-ts
mutations present in cpRSV are attenuating mutations for
seropositive humans (Connors et al., Virology, 208:478-84 (1995),
Firestone, et al., Virology, 225:419-522 (1996), Friedewald et al.,
JAMA, 203:690-694 (1968), Kim et al., Pediatrics, 48:745-755
(1971), each incorporated herein by reference). These and other
mutations are selected for their confirmed specificity for
attenuated and/or ts phenotypes using the methods described here,
and can then be assembled into a menu of attenuating mutations.
These and other attenuating mutations, both ts and non-ts, can then
be introduced into the RSV A2 wild-type virus to produce a live
attenuated virus selected for a proper balance between attenuation
and immunogenicity. In this regard, it is advantageous that the 530
and other identified ts mutations are not in the G and F
glycoproteins which induce the protective immune responses to RSV
in humans. This permits the development of an attenuated RSV cDNA
backbone with mutations outside of F and G that can serve as a cDNA
substrate into which the F and G glycoproteins of RSV subgroup B or
those of an epidemiologically divergent subgroup A strain can be
substituted for the A2 F and G glycoproteins. In this way, a live
attenuated RSV vaccine can be rapidly updated to accommodate
antigenic drift within subgroup A strains, and a subgroup B vaccine
component can also be rapidly produced.
EXAMPLE X
Construction of an Infectious Recombinant RSV Modified to
Incorporate Phenotype-Specific Mutations of RSV Strain
cpts248/404
This Example illustrates additional designs for introducing
predetermined attenuating mutations into infectious RSV employing
the recombinant procedures and materials described herein.
Previous sequence analysis of the RSV A2 cpts248 mutant also
identified a single mutation in the L gene, a glutamine to leucine
substitution at amino acid position 831 (Table 39; Crowe et al.,
Virus Genes, 13:269-273 (1996), incorporated herein by reference).
This mutation was confirmed by the methods herein to be attenuating
and ts. Sequence analysis of the further attenuated RSV mutant
cpts248/404 revealed two additional mutations, a nt change in the
M2 gene start sequence and an amino acid substitution, aspartic
acid to glutamic acid at amino acid position 1183 in the L protein
(Table 39; Firestone, et al., Virology, 225:419-522 (1996),
incorporated herein by reference).
The biologically-derived attenuated RSV strain cpts248/404 was
reconstructed as a recombinant virus (rA2 cp/248/404) according to
the above described methods. cDNA D53 encoding rA2 cp/248/404 virus
was constructed by insertion of the sites, HEK, cp, 248 and 404
changes (Table 39). Recombinant virus (rA2 cp/248/404) was
recovered, plaque purified and amplified. The presence of the
mutations in recombinant virus was analyzed by RT-PCR of viral RNA
followed by restriction enzyme digestion or nucleotide sequencing
or both. The rA2 cp/248/404 recombinant was recovered using either
the pTMLwt or pTML248/404 support plasmid, the latter of which
contains all of the mutations in L present in the biologically
derived cpts248/404 mutant (Table 39, not including the mutations
specific to the 530, 1009, or 1030 viruses). Using the pTML248/404
as a support plasmid precludes loss of 248/404 mutations present in
a full length clone by homologous recombination with the support
plasmid.
Recombinant viruses were recovered from D53 DNA in which only the
sites and HEK mutations were present (rA2 in Table 41), to
demonstrate that these changes were indeed phenotypically silent as
expected. Recombinant virus containing the sites, HEK and cp
mutations was recovered (called rA2 cp in Table 41), to evaluate
the phenotypes specified by the cp mutations. Also, as shown in
Table 41, separate viruses were constructed containing the sites,
HEK and cp background together with (i) the 248 mutation (rA2
cp/248), (ii) the two 404 mutations (rA2 cp/404); and the 404(M2)
mutation (rA2 cp/404(M2), and the 404(L) mutation (rA2 cp/404
(L)).
These viruses were evaluated in parallel for the ability to form
plaques in HEp-2 cells at 32.degree. C., 36.degree. C., 37.degree.
C., 38.degree. C. and 39.degree. C. This comparison showed that all
viruses formed plaques at 32.degree. C., and showed that the titers
of the various virus preparations were within approximately three
log.sub.10 units of each other, which is within the range of
experimental variation typically seen among independent
preparations of RSV. The introduction of the added "sites" and HEK
mutations into wild-type recombinant virus (to yield virus rA2) did
not alter the virus with regard to its ability to grow at the
elevated temperatures, as compared with biologically-derived
wild-type virus (virus A2 wt). The additional introduction of the
cp mutations (to yield virus rA2 cp) also did not alter its ability
to grow at elevated temperatures. This is the expected result,
because the biologically derived cpRSV from which the mutations
were derived does not have the ts phenotype; its mutations are of
the host range variety. The 404 mutation in L does not appear to be
a ts mutation since rA2 cp/404(L) was not ts. However, this
mutation may otherwise prove to be attenuating, as will be
determined by further analysis in accordance with the methods
herein. Thus, of the two specific mutations in cpts 248/404 virus
only the 404M2 mutation is ts. The further addition of the 248 and
404 mutations (to yield rA2 cp/248/404 virus) resulted in a ts
phenotype that was essentially equivalent to its
biologically-derived equivalent virus as evidenced by being greatly
impaired in the ability to form plaques at 36.degree. C.-37.degree.
C., with pinpoint plaques being formed at the former temperature.
These recombinant viruses incorporated a variety of mutations
predicted to have no effect on growth in tissue culture, and
additional mutations expected to confer a ts phenotype. Each type
of mutation yielded results consistent with these expectations,
demonstrating that the RSV genome can be manipulated in a
reasonably predictable way.
TABLE-US-00041 TABLE 41 Efficiency of Plaque Formation of Selected
RSV Mutants Virus titer (log.sub.10pfu/ml) Shut- Trans- at
indicated temperature (.degree. C.) off Virus.sup.1 fectant 32 36
37 38 39 temp. A2 wt.sup.2 5.0 4.8 5.1 4.6 4.7 >39 rA2 14-1B-1A2
4.9 4.2 4.4 4.5 3.9 >39 rA2cp 12-2B-1B1 5.6 5.1 4.8 3.8 3.7
>39 rA2cp/248 12-6A-1A1 5.8 4.8* 4.0* <0.7 <0.7 38
rA2cp/404-L 16-1A-1A1 5.4 5.2 5.1 4.9 5.0 >39 rA2cp/404-M2
15-1A-1A1 4.9 <0.7 <0.7 <0.7 <0.7 36 rA2cp/404
16-4B-1B1 3.3 1.2* <0.7 <0.7 <0.7 36 rA2cp/248/404 32-6A-2
6.0 <0.7 <0.7 <0.7 <0.7 36 rA2cp/248/404/ 13-4B-3 5.7
4.7* 2.5* nd <0.7 37 530 cpts248/404 5.1 <0.7 <0.7 <0.7
<0.7 36 (WLVP).sup.2 .sup.1Recombinant (r) viruses have been
plaque purified and amplified in HEp-2 cells. Note that the stocks
of recombinant and biologically-derived viruses had not been
adjusted to contain equivalent amounts of pfu/ml: the level of
variation seen here is typical for RSV isolates at an early stage
of amplification from plaques. Each recombinant virus contains the
L-gene sites and the F-gene HEK mutations. The code in the
"Transfectant" column refers to the transfection and plaquing
history. .sup.2Biologically derived viruses: A2 wt and cpts248/404
(WLVP L16210B-150). *Pin-point plaque size
Table 41 shows further characterization of mutations specific to
the 248 and 404 mutagenesis steps. Specifically, viruses were
constructed using the sites, HEK and cp background with the
addition of: (i) the 248 mutation (to yield virus rA2 cp/248), (ii)
the two 404 mutations (virus rA2 cp/404); or the 404(M2) mutation
(virus rA2 cp/404(M2)) (Table 39). Each of these three viruses
exhibited the ts phenotype, providing direct identification of
these mutations as being ts. The 248 mutation provided a lower
level of temperature sensitivity, whereas the 404(M2) mutation was
highly ts and was not augmented by the addition of the 404(L)
mutation. It was remarkable that the 404(M2) mutation is ts, since
it is a point mutation in a transcription initiation, or gene start
(GS), signal, and this type of mutation has never been shown to be
ts.
EXAMPLE XI
Construction of Recombinant RSV Combining Predetermined Attenuating
Mutations From Multiple Attenuated Parent Viruses
The present Example illustrates a combinatorial design for
producing a multiply attenuated recombinant RSV (rA2
cp/248/404/530) which incorporates three attenuating mutations from
one biologically derived RSV strain (specifically cpts248/404) and
an additional attenuating mutation from another RSV strain
(cpts530). This recombinant RSV exemplifies the methods of the
invention for engineering stepwise attenuating mutations to fine
tune the level of attenuation in RSV vaccines, wherein multiple
mutations contribute to a further attenuated phenotype of the
vaccine strain and provide for enhanced genetic stability.
The cDNAs and methods of Examples 1.times. and X above were used to
construct a D53 cDNA containing the sites, HEK, cp, 248, 404 and
530 changes (Table 39). This involved a combination of attenuating
mutations from four separate biologically-derived viruses, namely
cpRSV, cpts248, cpts248/404 and cpts530. Recombinant virus (rA2
cp/248/404/530) was recovered, plaque purified and amplified. The
presence of the mutations was analyzed by RT-PCR of viral RNA
followed by restriction enzyme digestion or nucleotide sequencing
or both. rA2 cp/248/404/530 lacked the 248 mutation in L, but
possessed the 530 mutation and the other 248/404 mutation.
The rA2 cp/248/404 virus was evaluated for its ability to form
plaques in HEp-2 cells at 32.degree. C., 36.degree. C., 37.degree.
C, 38.degree. C. and 39.degree. C. as described above (Table 41).
All of viruses formed plaques at 32.degree. C. and were similar to
wild-type in the efficiency of growth at this temperature. The rA2
cp/248/404/530 virus was essentially equivalent to the
biologically-derived cpts248/404 virus with regard to the ts
phenotype, evidenced by being greatly impaired in the ability to
form plaques at 37.degree. C. Thus, the addition of the 530
mutation to the rA2 cp/248/404 background did not increase its ts
phenotype, however, the recombinant lacked the 248 mutation in
L.
Based on this and the foregoing Examples, the invention allows
recovery of a wide variety of recombinant viruses containing two or
more ts mutations from the set of mutations which have been
identified and confirmed from biologically derived RSV mutants, for
example the 248, 404, 530, 1009, or 1030 biological mutants.
Examples of such recombinant viruses include RSV having a
combination of 248/404/530 mutations, 248/404/1009 mutations,
248/404/1030 mutations, 248/404/530/1009 mutations,
248/404/530/1030 mutations, 248/404/530/1030 mutations,
248/404/1009/1030 mutations, or other combinations of attenuating
mutations disclosed herein. In addition, recombinant RSV
incorporating one or more ts mutations identified from biologically
derived RSV mutants can be combined with other mutations disclosed
herein, such as attenuating gene deletions or mutations that
modulate RSV gene expression. One such example is to combine
248/404 mutations with an SH gene deletion in a recombinant clone,
which yields a viable vaccine candidate. A host of other
combinatorial mutants are provided as well, which can incorporate
any one or more ts mutations from biologically derived RSV and any
one or more other mutations disclosed herein, such as deletions,
substitutions, additions and/or rearrangements of genes or gene
segments. The cp mutations, which are attenuating host range rather
than attenuating ts mutations, also can be included along with one
or more other mutations within the invention. This provides a panel
of viruses representing a broad spectrum in terms of individual and
combined levels of attenuation, immunogenicity and genetic
stability. These attenuating mutations from biologically derived
RSV mutants can be further combined with the various other
structural modifications identified herein, which also specify
desired phenotypic changes in recombinant RSV, to yield yet
additional RSV having superior vaccine characteristics.
EXAMPLE XII
Recovery of Infectious Respiratory Syncytial Virus Expressing An
Additional, Foreign Gene
The methods described above were used to construct recombinant RSV
containing an additional gene, encoding chloramphenicol acetyl
transferase (CAT). The CAT coding sequence was flanked by
RSV-specific gene-start and gene-end motifs, the transcription
signals for the viral RNA-dependent RNA polymerase. Kuo et al., J.
Virol. 70:6892-6901 (1996) (incorporated herein by reference). The
RSV/CAT chimeric transcription cassette was inserted into the
intergenic region between the G and F genes of the complete
cDNA-encoded positive-sense RSV antigenome, and infectious
CAT-expressing recombinant RSV was recovered. The CAT mRNA was
efficiently expressed and the levels of the G and F mRNAs were
comparable to those expressed by wild-type recombinant RSV. The
CAT-containing and wild-type viruses were similar with regard to
the levels of synthesis of the major viral proteins.
Plasmid D46 was used for construction of cDNA encoding RSV
antigenomic RNA containing the CAT gene. (Plasmids D46 and D53, the
latter being described above, are different preparations of the
same antigenome cDNA.) D46 which encodes the complete,
15,223-nucleotide RSV antigenome (one nucleotide longer than that
of wild-type RSV) and was used to produce recombinant infectious
RSV, as described above. During its construction, the antigenome
cDNA had been modified to contain four new restriction sites as
markers. One of these, a StuI site placed in the intergenic region
between the G and F genes (positions 5611-5616 in the 3'-5'
sequence of the wild-type genome), was chosen as an insertion site
for the foreign CAT gene. A copy of the CAT ORF flanked on the
upstream end by the RSV GS signal and on the downstream end by the
RS GE signal was derived from a previously-described RSV-CAT
minigenome (Collins et al., Proc. Natl. Acad. Sci. USA 88:9663-9667
(1991) and Kuo et al., J. Virol. 70:6892-6901 (1996), incorporated
by reference herein). The insertion of this RSV/CAT transcription
cassette into the StuI site yielded the D46/1024CAT cDNA (deposited
under the terms of the Budapest Treaty with the ATCC and granted
the accession number VR-2544), which increased the length of the
encoded antigenome to a total of 15,984 nucleotides. And, whereas
wild-type RSV encodes ten major subgenomic mRNAs, the recombinant
virus predicted from the D46/1024CAT antigenome would encode the
CAT gene as an eleventh mRNA. The strategy of construction is shown
in FIG. 6.
Producing infectious RSV from cDNA-encoded antigenomic RNA, as
described above, involved coexpression in HEp-2 cells of five cDNAs
separately encoding the antigenomic RNA or the N, P, L or M2(ORF1)
protein, which are necessary and sufficient for viral RNA
replication and, transcription. cDNA expression was driven by T7
RNA polymerase supplied by a vaccinia-T7 recombinant virus based on
the MVA strain. The MVA-T7 recombinant virus produced infectious
progeny sufficient to cause extensive cytopathogenicity upon
passage, and therefore, cytosine arabinoside, an inhibitor of
vaccinia virus replication, was added 24 h following the
transfection and maintained during the first six passages. The use
of cytosine arabinoside was not required, however, and was not used
in later examples herein.
Two antigenome cDNAs were tested for the recovery of RSV: the D46
cDNA, and the D46/1024CAT cDNA. Each one yielded infectious
recombinant RSV. Cells infected with the D46/1024CAT recombinant
virus expressed abundant levels of CAT enzyme. For each virus,
transfection supernatants were passaged to fresh cells, and a total
of eight serial passages were performed at intervals of five to six
days and a multiplicity of infection of less than 0.1 PFU per
cell.
The CAT sequence in the D46/1024CAT genome was flanked by RSV GS
and GE signals, and thus should be expressed as an additional,
separate, polyadenylated mRNA. The presence of this predicted mRNA
was tested by Northern blot hybridization of RNA from cells
infected with D46/1024CAT virus or D46 virus at the eighth passage.
Hybridization with a negative-sense CAT-specific riboprobe detected
a major band which was of the appropriate size to be the predicted
CAT mRNA, which would contain 735 nucleotides not including
poly(A). This species was efficiently retained by oligo(dT) latex
particles, showing that it was polyadenylated. In some cases, a
minor larger CAT-specific species was detected which was of the
appropriate size to be a G-CAT readthrough mRNA. The D46/1024CAT
virus had been subjected to eight passages at low multiplicity of
infection prior to the infection used for preparing the
intracellular RNA. There was no evidence of shorter forms of the
CAT mRNA, as might have arisen if the CAT gene was subject to
deletion.
Replicate blots were hybridized with negative-sense riboprobe
specific to the CAT, SH, G or F gene, the latter two genes flanking
the inserted CAT gene. The blots showed that the expression of the
subgenomic SH, G and F mRNAs was similar for the two viruses.
Phosphoimagery was used to compare the amount of hybridized
radioactivity in each of the three RSV mRNA bands for D46/1024CAT
and D46. The ratio of radioactivity between D46/1024CAT and D46 was
determined for each mRNA: SH, 0.77; G, 0.87; and F, 0.78. The
deviation from unity probably indicates that slightly less RNA was
loaded for D46/1024CAT versus D46, although it is also possible
that the overall level of mRNA accumulation was slightly less for
D46/1024CAT RSV. The demonstration that the three ratios were
similar confirms that the level of expression of each of these
mRNAs was approximately the same for D46/1024CAT versus D46. Thus,
the insertion of the CAT gene between the G and F genes did not
drastically affect the level of transcription of either gene.
To characterize viral protein synthesis, infected HEp-2 cells were
labeled with [.sup.35S]methionine, and cell lysates were analyzed
by PAGE either directly or following immunoprecipitation under
conditions where recovery of labeled antigen was essentially
complete. Precipitation with a rabbit antiserum raised against
purified RSV showed that the D46/1024CAT and D46 viruses both
expressed similar amounts of the major viral proteins Fl, N, P, M,
and M2. That a similar level of M2 protein was recovered for each
virus was noteworthy because its gene is downstream of the inserted
CAT gene. Accumulation of the F protein, which is encoded by the
gene located immediately downstream of the insertion, also was
examined by immunoprecipitation with a mixture of three anti-F
monoclonal antibodies. A similar level of the F.sub.1 subunit was
recovered for each virus. Phosphorimagery analysis of the major
viral proteins mentioned above was performed for several
independent experiments and showed some sample-to-sample
variability, but overall the two viruses could not be distinguished
on the basis of the level of recovered proteins. Precipitation with
anti-CAT antibodies recovered a single species for the D46/1024CAT
but not for the D46 virus. Analysis of the total labeled protein
showed that the N, P and M proteins could be detected without
immunoprecipitation (although detection of the latter was
complicated by its comigration with a cellular species) and
confirmed that the two viruses yielded similar patterns. The
position corresponding to that of the CAT protein contained more
radioactivity in the D46/1024CAT pattern compared to that of D46,
as was confirmed by phosphorimagery of independent experiments.
This suggested that the CAT protein could be detected among the
total labeled proteins without precipitation, although this
demonstration was complicated by the presence of a comigrating
background band in the uninfected and D46-infected patterns.
RT-PCR was used to confirm the presence of the CAT gene in the
predicted location of the genome of recombinant RSV. Total
intracellular RNA was isolated from the cell pellet of passage
eight of both D46/1024CAT and D46 RSV. Two primers were chosen that
flank the site of insertion, the StuI restriction endonuclease site
at RSV positions 5611-5616: the upstream positive-sense primer
corresponded to positions 5412-5429, and the downstream
negative-sense one to positions 5730-5711. The positive-sense
primer was used for the RT step, and both primers were included in
the PCR.
RT-PCR of the D46 virus yielded a single product that corresponded
to the predicted fragment of 318 nucleotides, representing the G/F
gene junction without additional foreign sequence. Analysis of
D46/1024CAT viral RNA yielded a single product whose
electrophoretic mobility corresponded well with the predicted 1079
nucleotide fragment, representing the G/F gene junction containing
the inserted CAT transcription cassette. The latter PCR yielded a
single major band; the absence of detectable smaller products
indicated that the population of recombinant genomes did not
contain a large number of molecules with a deletion in this region.
When PCR analysis was performed on D46/1024CAT virus RNA without
the RT step, no band was seen, confirming that the analysis was
specific to RNA. Thus, the RT-PCR analysis confirmed the presence
of an insert of the predicted length in the predicted location in
the genomic RNA of the D46/1024CAT recombinant virus.
Enzyme expression was used to measure the stability of the CAT
gene. Cell pellets from all of the passages beginning with the
third were tested for CAT expression. For the virus D46/1024CAT,
all these assays displayed conversion of [.sup.14C] labeled
chloramphenicol into acetylated forms. To investigate stability of
expression, virus from 20 or 25 individual plaques from passage
three or eight, respectively, was analyzed for CAT expression. All
samples were positive, and the level of expression of CAT was
similar for each of the 25 isolates from passage eight, as judged
by assay of equivalent aliquots of cell lysate. This demonstrated
that the activity of the CAT protein encoded by each isolate
remained unimpaired by mutation.
To determine plaque morphology and size, beginning with the second
passage, one-eighth of the medium supernatant (i.e., 0.5 ml)
harvested from each passage stage was used to infect fresh HEp-2
cells in six-well plates that were incubated under methylcellulose
overlay for five to seven days. The cells were then fixed and
stained by incubation with monoclonal antibodies against RSV F
protein followed by a second antibody linked to horseradish
peroxidase. Earlier, it had been observed that recombinant RSV
produced from cDNA D46 was indistinguishable from a naturally
occurring wild-type RSV isolate with regard to efficiency of plaque
formation over a range of temperatures in vitro, and the ability to
replicate and cause disease when inoculated into the respiratory
tract of previously uninfected chimpanzees. Thus, the D46
recombinant RSV was considered to be a virulent wild-type strain.
The plaques produced by the D46 and D46/1024CAT recombinant viruses
were compared by antibody staining. Plaque morphology was very
similar for the two viruses, although the average diameter of the
CAT-containing recombinant plaques was 90 percent of that of the
D46 virus, based on measurement of thirty randomly-selected plaques
for each virus.
The efficiency of replication in tissue culture of the D46 and
D46/1024CAT viruses was compared in a single step growth cycle.
Triplicate monolayers of cells were infected with either virus, and
samples were taken at 12 h intervals and quantitated by plaque
assay. The results showed that the production of D46/1024CAT virus
relative to D46 was delayed and achieved a maximum titer which was
20-fold lower.
These results show that it is possible to construct recombinant,
helper-independent RSV expressing a foreign gene, in this instance
the CAT gene. The recombinant RSV directed expression of the
predicted polyadenylated subgenomic mRNA that encoded CAT protein,
the protein being detected both by enzyme assay and by
radioimmunoprecipitation. Other examples have produced RSV
recombinants with the luciferase gene inserted at the same CAT
site, or with the CAT or luciferase genes inserted between the SH
and G genes. These viruses also exhibit reduced growth, whereas the
numerous wild-type recombinant viruses recovered exhibit
undiminished growth. This indicates that the reduced growth indeed
is associated with the inserted gene rather than being due to
chance mutation elsewhere in the genome. The level of attenuation
appears to increase with increasing length of the inserted gene.
The finding that insertion of a foreign gene into recombinant RSV
reduced its level of replication and was stable during passage in
vitro suggests that this provides yet another means for effecting
attenuation for vaccine use. Also, the insertion into recombinant
RSV of a gene expressing a protein having antiviral activity, such
as gamma interferon and IL-2, among others, will yield attenuation
of the virus due to activity of the expressed antiviral
protein.
In addition to demonstrating recovery of RSV having modified growth
characteristics, the examples herein illustrate other important
methods and advantages for gene expression of recombinant RSV and
other nonsegmented, negative strand viruses. For example, the data
provided herein show that foreign coding sequences can be
introduced as a separate transcription cassette which is expressed
as a separate mRNA. These results also show that RSV is tolerant of
substantial increases in genome length, e.g., of 762 nucleotides in
the case of the CAT gene to a total of 15,984 nucleotides (1.05
times that of wild-type RSV). The luciferase gene that was
successfully recovered is almost three times longer.
The viral RNA-dependent RNA polymerases are known to have an
error-prone nature due to the absence of proofreading and repair
mechanisms. In RNA virus genomes, the frequency of mutation is
estimated to be as high as 10.sup.-4-10.sup.-5 per site on average
(Holland et al., Curr. Top. Microbiol. Immunol. 176:1-20 (1992) and
references therein). In the case of the recombinant D46/1024CAT RSV
produced here, correct expression of the foreign gene would be
irrelevant for virus replication and would be free to accumulate
mutations. The passages described here involved a multiplicity of
infection less than 0.1 PFU per cell, and the duration of each
passage level indicated that multiple rounds of infection were
involved. While yields of infectious virus from RSV-infected tissue
culture cells typically are low, intracellular macromolecular
synthesis is robust, and the poor yields of infectious virus seem
to represent an inefficient step in packaging rather than low
levels of RNA replication. Thus, the maintenance of CAT through
eight serial passages involved many rounds of RNA replication. It
was surprising that the nonessential CAT gene remained intact and
capable of encoding fully functional protein in each of the 25
isolates tested at the eighth passage. Also, RT-PCR analysis of RNA
isolated from passage eight did not detect deletions within the CAT
gene.
A second infectious RSV-CAT recombinant was constructed in which
the CAT transcription cassette was inserted into an XmaI site which
had been engineered into the SH-G intergenic region (which is one
position closer to the promoter than the F-G intergenic used
above). The growth characteristics of this recombinant were similar
to those of the D46/1024 CAT recombinant, whereas the level of CAT
expression was approximately two to three-fold higher, consistent
with its more promoter-proximal location. This illustrates that a
foreign gene can be inserted at a second, different site within the
genome and its level of expression altered accordingly. In
principle, any portion of the genome should be able to accept the
insertion of a transcription unit encoding a foreign protein as
long as the insertion does not disrupt a mRNA-encoding unit and
does not interfere with the cis-acting sequence elements found at
both ends of the genome.
An infectious recombinant RSV was also recovered in which the CAT
gene was replaced by that of the luciferase (LUC) marker enzyme.
The LUC coding sequence is approximately 1,750 bp (three times the
size of CAT), and is larger than any of the RSV genes except for F
and L. It was inserted at either the SH-G or G-F intergenic regions
and infectious recombinant virus was recovered. The LUC viruses
were further attenuated relative to the CAT viruses with regard to
growth in tissue culture, suggesting that increases in the size of
the genome lead to decreases in growth efficiency. Characterization
of these CAT and LUC viruses will determine the effect of foreign
gene size on virus gene expression and growth, such as how much is
due to the introduction of the additional set of transcription
signals, and how much is due to increased genome length.
In the minireplicon system, an RSV-CAT minigenome was modified such
that the transcriptional unit is in the "sense" orientation in the
positive-sense antigenome rather than the minigenome. Thus,
subgenomic mRNA can be made only if the polymerase is capable of
transcription of the antigenome replicative intermediate.
Interestingly, when complemented by plasmid-expressed N, P, L and
M2 ORF1 protein, this inverse RSV-CAT minigenome was capable of
synthesizing subgenomic, polyadenylated, translatable mRNA.
Efficient mRNA synthesis was dependent on the M2 ORF1 protein, as
is the case for minigenome transcription. The level of mRNA
relative to its antigenome template was approximately the same as
the ratio of mRNA to minigenome template made by a standard
minireplicon. This
indicates that the antigenome, as well as the genome, can be used
to accept a foreign transcriptional unit. Thus, expression of a
foreign gene can be achieved without placing it into the genome
transcriptional order. This had the advantage that the foreign gene
is not be part of the transcriptional program of the genome and
thus will not perturb the relative levels of expression of these
genes.
Because most of the antigenic difference between the two RSV
antigenic subgroups resides in the G glycoprotein, recombinant RSV
can be constructed to express the G protein of the heterologous
subgroup as an additional gene to yield a divalent vaccine.
Envelope protein genes of some other respiratory viruses, such as
human parainfluenza 3 virus, also can be inserted for expression by
recombinant RSV. Other uses include coexpression of immune
modulators such as interleukin 6 to enhance the immunogenicity of
infectious RSV. Other uses, such as employing modified RSV as
described herein as a vector for gene therapy, are also
provided.
EXAMPLE XIII
Recombinant RSV Having a Deletion of the SH Gene
This example describes production of a recombinant RSV in which
expression of the SH gene has been ablated by removal of a
polynucleotide sequence encoding the SH mRNA and protein. The SH
protein is a small (64 amino acids in the case of strain A2)
protein which contains a putative transmembrane domain at amino
acid positions 14-41. It is oriented in the membrane with the
C-terminus exposed and there is a potential glycosylation site in
both the C-terminal and N-terminal domains (Collins et al., J. Gen.
Virol. 71:3015-3020 (1990), incorporated herein by reference). In
infected cells, the SH protein of strain A2 accumulates in four
major forms; (i) SH0 (Mr 7500), the full-length, unglycosylated
form that is the most abundant (Olmsted et al., J. Virol.
63:2019-2029 (1989), incorporated herein by reference); (ii) SHg
(Mr 13,000-15,000), which is the full length form containing a
single N-linked carbohydrate chain; (iii) SHp (Mr 21,000-40,000),
which is a modified version of SHg in which the single N-linked
carbohydrate chain is modified by the addition of
polylactosaminoglycan (Anderson et al., Virology 191:417-430
(1992), incorporated herein by reference); (iv) SHt (Mr 4800), a
truncated unglycosylated form which is initiated from the second
methionyl codon (position 23) and which alone among the different
forms does not appear to be transported to the cell surface. The
SHO and SHp forms have been detected in purified virions,
suggesting that there is a selectivity at the level of virion
morphogenesis (Collins et al., supra, (1993)).
Among the paramyxoviruses, ostensibly similar SH proteins have been
found in simian virus 5 (Hiebert et al., J. Virol. 55:744-751
(1985), incorporated herein by reference), bovine RSV (Samal et
al., J. Gen. Virol. 72:1715-1720 (1991), incorporated herein by
reference), mumps virus (Elango et al., J. Virol. 63:1413-1415
(1989), incorporated herein by reference), and turkey
rhinotracheitis virus (Ling et al., J. Gen. Virol. 73:1709-1715
(1992), incorporated herein by reference). The small hydrophobic
VP24 protein of filoviruses is thought to be a surface protein
(Bukreyev et al., Biochem. Mol. Biol. Int. 35:605-613 (1995),
incorporated herein by reference) and is also a putative
counterpart of the paramyxovirus SH protein.
The function of the SH protein has not been heretofore defined. In
a fusion assay in cells expressing plasmid-encoded proteins,
efficient fusion of CV-1 cells by RSV proteins required the
coexpression of the F, G and SH proteins (Heminway et al., Virology
200:801-805 (1994), incorporated herein by reference). Without
wishing to be bound by theory, several functions of the RSV SH
protein may exist: (i) it may enhance viral attachment or
penetration (Heminway et al., supra.); (ii) it may be involved in
virion morphogenesis; or (iii) it may have a "luxury" function
distinct from a direct role in virus growth, such as interaction
with components of the host immune system as recently described for
the V protein of Sendai virus (Kato et al., EMBO J. 16:178-587
(1997), incorporated herein by reference). Function (i) or (ii)
above may involve an activity that modifies membrane permeability,
as has been suggested by others for some hydrophobic proteins of
various viruses (Maramorosh et al. (eds.), Advances in Virus
Research 45:61-112 (1995); Schubert et al., FEBS Lett. (1996); Lamb
et al., Virology 229:1-11 (1997), each incorporated herein by
reference). All of these potential activities of the SH protein may
be incorporated within the invention according to the methods and
strategies described herein, to yield additional advantages in RSV
recombinant vaccines.
To produce a recombinant RSV having a selected disruption of SH
gene function, the SH gene was deleted in its entirety from a
parental RSV clone. The above described plasmid D46 plasmid is one
such clone which encodes a complete antigenomic RNA of strain A2 of
RSV, which was used successfully to recover recombinant RSV (See
U.S. patent application Ser. No. 08/720/132; U.S. Provisional
Patent Application No. 60/007,083, each incorporated herein by
reference). This antigenome is one nt longer than the
naturally-occurring genome and contains several optional
restriction site markers. The D46 plasmid was modified so that the
complete SH gene was deleted, yielding plasmid D46/6368 (FIG.
7).
The construction of plasmid D46/6368 involved two parental
subclones, D50, which contains a T7 promoter attached to the
left-hand end of the genome encompassing the leader region to the
beginning of the L gene, and D39, which contains the end of M2 and
the L gene attached at the downstream end to a hammerhead ribozyme
and tandem T7 transcription terminators. The D50 plasmid was
digested with ScaI (position 4189 in the complete 15,223-nucleotide
antigenome sequence) and PacI (position 4623) and the resulting 435
bp fragment was replaced with a short DNA fragment constructed from
two complementary oligonucleotides. In this exemplary deletion, the
435-bp fragment located between the ScaI and PacI sites corresponds
to the very downstream end of the M gene, its GE signal, and the
complete SH gene except for the last six nucleotides of its GE
sequence (FIG. 7). This was replaced with the two synthetic
partially complementary oligonucleotides,
5'-ACTCAAATAAGTTAATAAAAAATATCCCGGGAT-3' [SEQ ID NO: 3]
(positive-sense strand, the M GE sequence is underlined, Xmal site
is shown in italics, and the ScaI half-site and PacI sticky end at
the left and right respectively are shown in bold italics) and
5'-CCCGGGATATTTTTTATTAACTTATTTGAGT-3' [SEQ ID NO: 4]
(negative-sense strand). This cDNA, called D50/6368, was used to
accept the BamHI-Mlul fragment of D39 containing the remainder of
the antigenome. This resulted in the plasmid D46/6368 which encoded
the complete antigenome except for the deleted sequence, an
antigenome that is 14,825 nt long, 398 nt shorter than the
antigenome encoding by the wild-type plasmid D46. The sequence of
the insert was confirmed by dideoxynucleotide sequence analysis. An
XmaI site was optionally introduced so that inserts could easily be
placed at this position in subsequent work.
Transfection, growth and passaging of virus, plaque purification,
and antibody staining of viral plaques were generally performed
according to the procedures described hereinabove, but with two
modifications: (i) cytosine arabinoside, an inhibitor of vaccinia
virus was not used; (ii) HEp-2 cells used for transfection were
incubated at either 32.degree. C. or 37.degree. C., and all
recovered viruses were propagated at 37.degree. C.
To evaluate total RNA and poly(A)+ RNA, cells were scraped and
resuspended in 100 .mu.l of water, and total intracellular RNA was
isolated using Trizol.TM. reagent (Life Technologies) according the
manufacturer's recommendation (except that following isopropanol
precipitation the RNA was extracted twice with phenol-chloroform
followed by ethanol precipitation. Poly(A)+ RNA was isolated using
the Oligotex mRNA kit (Qiagen, Chatsworth, Calif.).
To conduct reverse transcription and polymerase chain reaction
(RT-PCR), the SH gene region was copied into cDNA and amplified.
Total intracellular RNA was subjected to reverse transcription with
Superscript II (Life Technologies) using as primer the positive
sense synthetic oligonucleotide 5'-GAAAGTATATATTATGTT-3' [SEQ ID
NO: 5]. This primer is complementary to nucleotides 3958-3975,
which are upstream of the SH gene. An aliquot of the cDNA product
was used as template in PCR using as primer the above-mentioned
oligonucleotide together with the negative-sense oligonucleotide
5'-TATATAAGCACGATGATATG-3' [SEQ ID NO:6]. This latter primer
corresponds to nucleotides 4763-4782 of the genome, which are
downstream the SH gene. An initial 2 min. denaturation step was
performed during which the Taq DNA polymerase was added, and then
33 cycles were performed (denaturation, 1 min. at 94.degree. C.;
annealing, 1 min. at 39.degree. C.; elongation, 2 min. at
72.degree. C.). The products were then analyzed on a 2.5% agarose
gel.
For Northern blot hybridization, RNA was separated by
electrophoresis on agarose gels in the presence of formaldehyde and
blotted to nitrocellulose. The blots were hybridized with
[.sup.32P]-CTP-labeled DNA probes of the M, SH, G, F, M2 and L
genes which were synthesized individually Ln vitro from cDNAs by
Klenow polymerase with random priming using synthetic hexamers
(Boehringer Mannheim, Indianapolis, Ind.). Hybridized radioactivity
was quantitated using the Molecular Dynamics (Sunnyvale, Calif.)
Phosphorlmager 445 SI.
.sup.35S methionine labeling, immunoprecipitation, and
polyacrylamide gel electrophoresis procedures were performed as
described previously (Bukreyev et al., supra). Electrophoresis was
conducted using pre-cast 4%-20% Tris-glycine gels (Novex).
For In vitro growth analysis, HEp-2, 293, CV-1, Vero, MRC-5,
African green monkey kidney (AGMK), bovine turbinate (BT), and MDBK
cell monolayers were used in a single-step growth cycle analysis.
For each type of cells, three 25-cm.sup.2 culture flasks were
infected with 10.sup.7 PFU of the D46/6368 (SH-minus) or D46
(wild-type recombinant) virus. Opti-MEM (Life Technologies) with 2%
fetal bovine serum (FBS) (Summit) was used for HEp-2, Vero, 293,
BT, MRC-5, and AGMK cells; E-MEM (Life Technologies) with 1%, or 2%
FBS was used for MDBK or BT cells, respectively. After 3 hours
adsorption at 37.degree. C., cells were washed with 4 ml medium
three times each, 4 ml medium was added, and the cells were
incubated at 37.degree. C. with 5% CO.sub.2. Then, at various times
after inoculation (see below), 200 .mu.l aliquots of medium
supernatant were removed, adjusted to contain 100 mM magnesium
sulfate and 50 mM HEPES buffer (pH 7.5), flash-frozen and stored at
-70.degree. C. until titration; each aliquot taken was replaced
with an equal amount of fresh medium. For titration, HEp-2 cells
(24-well plates) were infected with 10-fold dilutions of aliquots,
and overlaid with Opti-MEM containing 2% FBS and 0.9%
methylcellulose (MCB Reagents). After incubation for 7 days, the
medium was removed and the cell monolayer was fixed with 80%
methanol at 4.degree. C. The plaques were incubated with a mixture
of three monoclonal antibodies specific to RSV F protein, followed
by goat anti-mouse IgG conjugated with horseradish peroxidase
(Murphy et al., Vaccine 8:497-502 (1990), incorporated herein by
reference).
Recovery of infectious, recombinant RSV lacking SH gene function
followed the above described procedures, wherein the D46/6368
plasmid was cotransfected into HEp-2 cells together with plasmids
encoding the N, P, L and M2 ORF1 proteins, and the cells were
simultaneously infected with a recombinant of the MVA strain of
vaccinia virus that expresses T7 RNA polymerase. Parallel cultures
were transfected with the D46 wild-type cDNA under the same
conditions. Medium supernatants were harvested three days
post-transfection and passaged once. After 6 days incubation at
37.degree. C., an aliquot of medium supernatant representing each
original transfection was plated onto fresh HEp-2 cells, incubated
for six days under methylcellulose overlay, and stained by reaction
with a mixture of three monoclonal antibodies specific to the RSV F
protein followed by a second antibody conjugated with horseradish
peroxidase. Morphology of plaques of wild-type recombinant virus
versus the SH-minus virus were very similar, except that the latter
plaques were larger. Notably, plaques formed by each of the control
and SH minus viruses contained syncytia.
To confirm the absence of the SH gene in the genome of recovered
D46/6368 virus, cells were infected with the first passage of
wild-type or SH-minus recombinant virus, and total intracellular
RNA was recovered and analyzed by RT-PCR. RT was performed with a
positive-sense primer that annealed upstream of the SH gene, at
genome positions 3958-3975. PCR was performed using the same primer
together with a negative-sense primer representing nucleotides
4763-4782, downstream of the SH gene. As shown in FIG. 8, wild-type
D46 virus yielded a single PCR product corresponding to the
predicted 824 bp fragment between positions 3958 and 4782 (lane 3),
In the case of the D46/6368 virus, the PCR product was shorter and
corresponded to the predicted 426 bp fragment containing the
deletion (lane 2). The generation of The PCR products was dependent
on the RT step, showing that they were derived from RNA rather than
DNA, as expected. Thus, RT-PCR analysis demonstrates that the
genome of D46/6368 virus contains the expected 398-nucleotide
deletion at the SH locus.
To examine the transcription of genes located upstream and
downstream the SH gene, poly(A)+ mRNA was isolated from cells
infected with the D46 or D46/6368 virus and analyzed by Northern
blot hybridization (FIG. 9). The intracellular RNA purposefully was
not denatured prior to poly(A)+ selection; thus, as shown below,
the selected mRNA also contained genomic RNA due to sandwich
hybridization to mRNA. This permitted simultaneous analysis of mRNA
and genome, and the ability to relate the abundance of each mRNA to
genomic RNA contained in the same gel lane made it possible to
compare mRNA abundance between lanes. The blots were hybridized
with [.sup.32P]-labeled DNA probes which were synthesized from cDNA
clones by random priming and thus contained probes of both
polarities. Selected probes represented individually the M, SH, G,
F, M2, and L genes (FIG. 9).
The SH probe hybridized to both subgenomic SH mRNA and genomic RNA
in the case of the wild-type D46 virus but not for the D46/6368
virus (FIG. 9). The probes specific for other RSV genes hybridized
in each case to the genome and to the expected major monocistronic
mRNA for both viruses. In addition, a number of previously
described dicistronic readthrough mRNAs also were detected with
both viruses, such as the F-M2, G-F and P-M mRNAs.
The G-specific probe hybridized to an novel species specific to the
D46/6368 virus, which appeared to be a readthrough of the M and G
genes. This combination was possible due to the deletion of the
intervening SH gene. The same species, specific to D46/6468 but not
D46, appeared to hybridize in addition only with the M-specific
probe.
Relative levels of synthesis were subsequently quantified for each
mRNA of D46 versus D46/6368. For each pairwise comparison, the
amount of mRNA in a given gel lane was normalized relative to the
amount of genome. This comparison showed D46/6368 versus D46
expressed the following mRNAs in the indicated ratio (D46/6368 to
D46): M (1.1), G (1.3), F (0.61), M2 (0.32), and L (0.17).
To compare viral proteins synthesized by D46 versus D46/6368 RSV
clones, HEp-2 cells were infected at an input multiplicity of
infection of 2 PFU per cell and labeled by incubation with
[.sup.35S]methionine from 16 to 20 h post-infection. Cell lysates
were prepared and analyzed directly or following
immunoprecipitation using a rabbit antiserum raised against
purified RSV virions. Total and immunoprecipitated proteins were
subjected to PAGE on 4-20% gradient gels (FIG. 10).
In the case of the D46 virus, the pattern of immunoprecipitated
proteins included the unglycosylated form of SH protein, SH0, and
the N-glycosylated form, SHg, whereas neither species was evident
for the D46/6368 virus (FIG. 10). The SH0 protein also could be
detected in the pattern of total infected-cell proteins in the case
of D46, but not D46/6368. Otherwise, the patterns of proteins
synthesized by D46 versus D46/6368 were essentially
indistinguishable. Phosphorimager analysis of the N, P, M, F.sub.1,
and M2 proteins in the pattern of immunoprecipitated proteins
showed that equivalent amounts were made by both viruses (FIG.
10).
As described above, preliminary comparison of the D46 and D46/6368
viruses by plaque assay indicated a difference in growth in vitro.
Therefore, we further compared the two viruses with regard to
plaque size in HEp-2 cells. Particular care was taken to ensure
that the monolayers were young and not overgrown, since these
variables can effect plaque size. After 7 days incubation at
37.degree. C. under methylcellulose, the monolayers were fixed with
methanol and photographed. This revealed a striking difference in
plaque size. Measurement of 30 plaques of each virus viruses showed
that the plaques of the D46/6368 virus were on average 70% larger
than those of the D46 virus.
Further experiments were undertaken to render a growth curve
analysis for eight different cell lines representing different
species and different tissue origins, to compare efficiencies of
replication of the D46 and D46/6368 viruses (Table 42). Triplicate
monolayers of each type of cell were infected with either virus,
and samples were taken at 12 or 24 hours intervals, and quantitated
by plaque assay and antibody staining. Surprisingly, the D46/6368
virus grew to higher titers relative to the D46 wild-type in three
cell lines, namely HEp-2, 293 and AGMK-21 cells. In HEp-2 cells
(FIG. 11), the titer of progeny D46/6368 virus at 36 hours post
infection was 2.6 fold greater than for the D46 virus. In 293 cells
(FIG. 12), the yield of D46/6368 virus was two fold greater than
that of the D46 virus at 36 hours post infection, and this
difference increased to 4.8 and 12.6-fold at 60 and 84 h post
infection, respectively. In AGMK-21 cells (FIG. 13), the yield of
D46/6368 virus was 3.2 times at 36 hours post infection. In MRC-5,
Vero, CV-1, MDBK and BT cells, a significant difference in
replication among mutant and wild-type virus was not observed,
indicating that the growth of SH-minus RSV was not substantially
affected by host range effects.
TABLE-US-00042 TABLE 42 Replication of D46/6368 Virus as Compared
to D46 Virus in Various Cell Lines D46/6368 Virus Replication As
Cell Type Host Tissue Type Compared to D46 HEp-2 human larynx
increased 293 human kidney increased MRC-5 human lung similar Vero
monkey kidney similar AGMK-21 monkey kidney increased CV-1 monkey
kidney similar BT bovine turbinate similar MDBK bovine kidney
similar
These and other findings herein demonstrate that deletion of the SH
gene yields not only recoverable, infectious RSV, but a recombinant
RSV which exhibits substantially improved growth in tissue culture,
based on both yield of infectious virus and on plaque size. This
improved growth in tissue culture specified by the SH deletion
provides useful tools for developing RSV vaccines, for example by
overcoming problems of poor RSV yields in culture. Moreover, these
deletions are highly stable against genetic reversion, rendering
RSV clones derived therefrom particularly useful as vaccine
agents.
To evaluate replication, immunogenicity and protective efficacy of
the exemplary SH-deletion clone in mice, respiratory-pathogen-free
13-week old BALB/c mice in groups of 24 were inoculated
intranasally under light methoxyflurane anesthesia on day 0 with
10.sup.6 PFU per animal in a 0.1 ml inoculum of wild-type
recombinant D46 virus, SH-minus recombinant D46/6368 virus, or
biologically-derived cold-passaged (cp) temperature-sensitive (ts)
virus cpts248/404 (Firestone et al., supra, (1996), incorporated
herein by reference). This latter virus has been extensively
characterized in rodents, chimpanzees and humans, and is highly
restricted in replication in the upper and lower respiratory tract
of the mouse. At each of days 4, 5, 6 and 8 post-inoculation, six
mice from each group were sacrificed by CO.sub.2 asphyxiation, and
nasal turbinates and lung tissue were obtained separately,
homogenized, and used in plaque assay for quantitation of virus
using the antibody staining procedure described above.
In the upper respiratory tract, the SH minus D46/6368 virus
exhibited an attenuation phenotype (FIG. 14). In the present
example, its level of replication was 10-fold lower than that of
the wild-type virus, and was comparable to that of the cpts248/404
virus. In contrast, in the lower respiratory tract (FIG. 15) the
level of replication of the D46/6368 virus was very similar to that
of the wild-type, whereas the cpts248/404 virus was highly
restricted. In additional studies, it was shown that the SH-minus
recombinant virus encoded by the parental D46 cDNA has a slightly
attenuated phenotype in the upper respiratory tract and a
moderately attenuated phenotype in the lower respiratory tract in
naive chimpanzees, a fully permissive experimental animal. This
mutant also elicited greatly reduced disease symptoms compared to
wild-type RSV in naive chimps, while stimulating significant
resistance to challenge by the wild-type virus. Whitehead et al.,
J. Virol. 73:(4)3438-3442 (1999), incorporated herein by
reference.
The foregoing data indicate that the parental recombinant virus,
assembled as it was from a laboratory strain, contains a full
complement of intact genes necessary for replication and virulence
in a permissive host. These and other properties of exemplary gene
deletion RSV strains render a host of methods and strains available
for vaccine use.
To further evaluate immunogenicity and protective efficacy of
recombinant RSV, four additional groups of mice were inoculated as
described above with wild-type recombinant, its SH-minus
derivative, or the cpts248/404 virus, or were mock infected. Four
weeks later the mice were anesthetized, serum samples were taken,
and a challenge inoculation of 10.sup.6 PFU of biologically-derived
RSV strain A2 per animal was administered intranasally. Four days
later the animals were sacrificed and nasal turbinates and lung
tissues were harvested and assayed for infectious RSV as described
above. Serum IgG antibodies which bind to the RSV F protein were
quantitated in an ELISA using F glycoprotein which had been
immunoaffinity-purified from RSV Long strain infected cells (Murphy
et al., supra, 1990).
The immunogenicity assays for the D46 wild-type, D46/6368 SH-minus,
and cpts248/404 viruses showed that mice which had been infected on
day 0 with any of the three viruses developed high levels of
F-specific serum antibodies (Table 43). All of these test hosts
were highly resistant in both the upper and lower respiratory
tracts to replication of RSV challenge virus. Thus, the SH-minus
mutant could not be distinguished from its wild-type parent on the
basis of its ability to induce RSV-specific serum antibodies and
protection in the mouse.
TABLE-US-00043 TABLE 43 The RSV D46/6368 SH-minus virus is
immunogenic and protects the upper and lower respiratory tract of
mice against wild-type challenge RSV A2 Replication after
challenge.sup.3 Serum antibody titer.sup.2 (mean log.sub.10pfu/g
tissue) Immunizing No. of (reciprocal mean log.sub.2) Nasal
Virus.sup.1 Mice Day 0 Day 28 turbinates Lungs D46.sup.4 6 7.3 15.0
<2.0 <1.7 D46/6368.sup.5 6 7.3 15.0 2.1 <1.7 cpts248/404 6
7.0 12.6 2.3 <1.7 none 6 7.6 7.3 4.6 5.1 .sup.1Groups of BALB/c
mice were immunized intranasally with 10.sup.6 pfu of the indicated
virus on day 0. .sup.2Serum IgG antibody response was quantitated
in an ELISA using immunopurified F glycoprotein from RSV subgroup
A. .sup.3Mice were intranasally administered 10.sup.6 pfu of RSV A2
on day 28 and sacrificed 4 days later. .sup.4Wild-type recombinant
virus. .sup.5SH-minus recombinant virus.
Comparisons of the SH genes of different RSVs and different
pneumoviruses provide additional tools and methods for generating
useful RSV recombinant vaccines. For example, the two RSV antigenic
subgroups, A and B, exhibit a relatively high degree of
conservation in certain SH domains. In two such domains, the
N-terminal region and putative membrane-spanning domains of RSV A
and B display 84% identity at the amino acid level, while the
C-terminal putative ectodomains are more divergent (approx. 50%
identity) (Collins et al., supra, 1990). Comparison of the SH genes
of two human RSV subgroup B strains, 8/60 and 18537, identified
only a single amino acid difference (Anderson et al., supra). The
SH proteins of human versus bovine RSV are approximately 40%
identical, and share major structural features including (i) an
asymmetric distribution of conserved residues similar to that
described above; (ii) very similar hydrophobicity profiles; (iii)
the presence of two N-linked glycosylation sites with one site
being on each side of the hydrophobic region; and (iv) a single
cysteine residue on the carboxyterininal side of the central
hydrophobic region of each SH protein. (Anderson et al., supra). By
evaluating these and other sequence similarities and differences,
selections can be made of heterologous sequence(s) that can be
substituted or inserted within infectious RSV clones, for example
to yield vaccines having multi-specific immunogenic effects.
Transcriptional analyses for D46 and D46/6368 yielded other
important findings within the present example. Overall
transcription levels were substantially the same for both viruses,
whereas, Northern blot analysis revealed certain differences in
accumulation of individual mRNA species. Notably, transcription of
the M gene, located upstream of the SH gene, was substantially the
same for the two viruses. However, deletion of the SH gene resulted
in increased transcription for its downstream neighbor, the G gene
(FIG. 16). Based on these results, transcriptional levels of
selected RSV genes can be modulated simply by changing the
respective polarities or proximity of genes on the RSV map. For
example, the D46 virus G gene is seventh in the gene order, whereas
deletion of the SH gene places it in the sixth position, resulting
in increased levels of transcription. The observed increase in
transcription associated with this change in gene order was less
than the 2.5 to 3-fold increase which has been reported in other
recombinant viral systems (see, e.g., Kuo et al., supra,
(1996)).
Another important finding revealed in the foregoing studies was
that each of the genes downstream of the G gene (F, M2 and L) was
expressed less efficiently in the SH-minus mutant, and there was a
steeper gradient of polarity for D46/6368 versus the wild-type D46
virus exhibited by these downstream genes (FIG. 16). Notably, the
engineered M-G intergenic region of D46/6368 that was left
following the SH deletion was 65 nt in length. In comparison, the
longest naturally-occurring intergenic regions in strain A2 are the
44-nt M-SH, 46-nt F-M2, and 52-nt G-F intergenic regions, and
strain 18537 has a F-M2 intergenic region of 56 nt (Johnson et al.,
J. Gen. Virol. 69:2901-2906 (1988), incorporated herein by
reference). The naturally-occurring intergenic regions of strain
A2, which range in size from one to 52 nt, did not substantially
differ with regard to their effect on transcriptional readthrough
and polarity in a dicistronic minigenome (Kuo et al, supra,
(1996)). However, testing of regions longer than the 52-nt G-F
region according to the methods of the invention may establish an
upper limit after which the polymerase is affected more severely.
Thus, the lower-than-expected increase in G gene transcription
resulting from the change in gene order observed in the SH-minus
deletion clones, as well as the reduced transcription of the
downstream genes, may be attributable to the greater length of the
intergenic region that was engineered between M and G. In this
regard, adjustment in the selected length of intergenic regions of
RSV clones within the invention is expected to provide yet
additional tools and methods for generating useful RSV
vaccines.
The above findings offer two additional methods for altering levels
of RSV gene expression. First, the deletion of a nonessential gene
can up-regulate the expression of downstream genes. Second, the
insertion of longer than wild-type intergenic regions provide
methods for decreasing the transcription of downstream genes.
Decreased levels of expression of downstream genes are expected to
specify attenuation phenotypes of the recombinant RSV in permissive
hosts, e.g., chimpanzees and humans.
The finding that the SH-minus virus grows well in tissue culture
and exhibits site-specific attenuation in the upper respiratory
tract presents novel advantages for vaccine development. Current
RSV strains under evaluation as live virus vaccines contain, e.g.,
cp mutations (acquired during extensive passage at progressively
lower temperatures; to yield cpRSV strains). Exemplary cp mutations
involve five amino acid substitutions in N, F and L, and do not
confer temperature-sensitivity or cold-adaptation. These mutations
further do not significantly affect growth in tissue culture. They
are host range mutations, because they restrict replication in the
respiratory tract of chimpanzees and humans approximately 100-fold
in the lower respiratory tract. Another exemplary type of mutation,
ts mutations, has been acquired by chemical mutagenesis of cpRSV.
This type of mutation tends to preferentially restrict virus
replication in the lower respiratory tract, due to the gradient of
increasing body temperature from the upper to the lower respiratory
tract. In contrast to these cp and ts mutants, the SH-minus mutants
described herein have distinct phenotypes of greater restriction in
the upper respiratory tract. This is particularly desirable for
vaccine viruses for use in very young infants, because restriction
of replication in the upper respiratory tract is required to ensure
safe vaccine administration in this vulnerable age group whose
members breath predominantly through the nose. Further, in any age
group, reduced replication in the upper respiratory tract will
reduce morbidity from otitis media. In addition to these
advantages, the nature of SH deletion mutations, involving e.g.,
nearly 400 nt and ablation of an entire mRNA, represents a type of
mutation which will be highly refractory to reversion.
EXAMPLE XIV
Recombinant RSV Having a Deletion of the SH Gene Without the
Introduction of Heterologous Sequence
This example describes the production of a recombinant RSV in which
expression of the SH protein has been ablated by removing a
polynucleotide sequence encoding the SH protein, without
introducing heterologous sequence as was done in the preceding
Example XIII. In that example, an RSV clone D46/6368 in which the
SH coding sequence had been removed also featured an M-G intergenic
region that was extended to 65 nucleotides in length compared to 52
nucleotides for the longest naturally occurring strain A2
intergenic region. Also, this engineered intergenic region
contained heterologous sequence including a SmaI site. These
changes yield certain advantageous results, such as reducing the
efficiency of transcription of downstream genes. However, for other
applications it is desirable to make deletions or changes which are
not accompanied by the introduction of heterologous sequence, as
illustrated in the present Example (FIG. 17).
The D13 plasmid, described hereinabove (see Example VII), contains
the T7 promoter attached to the left-hand end of the genome
encompassing the leader region, and the NS1, NS2, N, P, M, and SH
genes (sequence positions 1 to 4623 in the complete 15,223
antigenome sequence). The ScaI (position 4189) to PacI (position
4623) fragment was replaced with the two partially-complementary
synthetic oligonucleotides: ACTCAAATAAGTTAAT [SEQ ID NO:7]
(positive-sense strand, the ScaI half site is italicized to the
left and the PacI sticky end is italicized to the right, and part
of the GE signal is underlined), and TAACTTATTTGAGT [SEQ ID NO:8]
(negative sense, the ScaI half-site is italicized on the right, and
part of the GE signal is underlined). This mutation resulted in the
deletion of the M GE signal, the M-SH intergenic region and the
complete SH gene, and had the effect of moving the SH GE signal up
to replace that of the M gene. No heterologous nucleotides were
introduced. The resulting cDNA, called D13/6340, was ligated with
the G-F-M2 cDNA piece (see Example VII) to yield D50/6340, which
spans from the leader region to the beginning of the L gene.
The StuI-BamHI fragment of D50/6340 (spanning positions 5613 to
8501, including the F and M2 genes) was excised and replaced with
the equivalent fragment of D50-COR#l, which is isogenic except that
it contains the two "HEK" changes to the F gene described
hereinabove. The resulting D50/6340HEK was used to accept the
BamHI-MluI fragment of D39sites#12, which contains the remainder of
the antigenome cDNA and the flanking ribozyme and T7 transcription
terminators (see Example IX). D39sites#12 is a version of D39 which
contains the "sites" mutations (see Table 39). This resulted in
plasmid D46/6340HEK, encoding an antigenome lacking the SH gene and
containing the "HEK" and "sites" changes. The D46/6340 antigenome
cDNA is 417 bp shorter than its parental D46 cDNA. The sequence of
the ScaI PacI synthetic insert was confirmed by dideoxynucleotide
sequencing. The cDNA was then used successfully to recover
recombinant virus by the procedures described hereinabove. The
recovered D46/6340 SH deletion virus resembled the D46/6368 SH
deletion virus described in Example XIII on the basis of its plaque
phenotype and growth characteristics.
EXAMPLE XV
Knock-out of NS2 Protein Expression
This example illustrates ablation of synthesis of an RSV protein,
NS2. The selected method for ablation in this instance was
introduction of stop codons into a translational open reading frame
(ORF).
D13 is a cDNA representing the left hand end of the complete
antigenome cDNA, including the T7 promoter, leader region, and the
NS1, NS2, N, P, M and SH genes (sequence positions 1 to 4623) (FIG.
18). The AatII-AflII fragment of this cDNA, containing the T7
promoter and NS1 and NS2 genes, was subcloned into a pGem vector
and subjected to oligonucleotide-directed mutagenesis to introduce
two translational stop codons into the NS2 ORF together with an
XhoI site that was silent at the translational level and served as
a marker (FIG. 18). The sequence of the mutation was confirmed, and
the AatII-AflII fragment was inserted into D13, which was then
ligated with the PacI-BamHI fragment containing the G, F and M2
genes, to yield cDNA D50 containing the inserted mutations. This
was then ligated with the insert of D39 to yield a complete
antigenome cDNA which was used to recover recombinant virus. The
presence of the mutation in the recombinant RSV was confirmed by
sequencing of RT-PCR products and by XhoI digestion. In addition,
the absence of synthesis of NS2 protein was confirmed by Western
blot analysis using a rabbit antiserum raised against a synthetic
peptide representing the C-terminus of NS2.
FIG. 19 shows growth curves comparing the NS2-knock-out virus with
recombinant wild-type, using the methods described above for the
SH-minus virus. These results demonstrate that the rate of release
of infectious virus was reduced for the NS2-knock-out virus
compared to wild-type. In addition, comparison of the plaques of
the mutant and wild-type viruses showed that those of the
NS2-knock-out were greatly reduced in size. This type of mutation
can thus be incorporated within viable recombinant RSV to yield
altered phenotypes, in this case reduced rate of virus growth and
reduced plaque size in vitro. These and other knock-out methods and
mutants will therefore provide for yet additional recombinant RSV
vaccine agents, based on the known correlation between reduced
plaque size in vitro and attenuation in vivo.
EXAMPLE XVI
Modulation of RSV Phenotype by Alteration of Cis-Acting Regulatory
Sequence Elements
This example illustrates modulation of growth properties of a
recombinant RSV virus by altering cis-acting transcription signals
of exemplary genes, NS1 and NS2.
The subcloned AatII-AflII fragment of D13, representing the
lefthand end of the genome, was subjected to
oligonucleotide-directed mutagenesis to introduce changes at the GE
signals of the NS1 and NS2 genes (FIG. 20). The NS1 GE signal
sustained a single nucleotide substitution, whereas that of NS2
sustained three substitutions and one insertion. These changes had
the effect of altering each signal to be identical to the
naturally-occurring GE signal of the N gene.
These mutations were confirmed by dideoxynucleotide sequence
analysis, and the AatII-flII fragment was replaced into D13, which
in turn was taken through the above described steps to construct a
complete D53 DNA containing the mutations. This clone was used to
recover recombinant virus.
The GE-mutant virus was analyzed in HEp-2 cells and compared to
wild-type virus with respect to plaque size and growth curve. This
showed that the plaques were larger (on average 30% greater) than
those of wild-type, and the rate of growth and yield of virus were
increased. These results are consistent with modification of gene
expression by altering cis-regulatory elements, for example to
decrease levels of readthrough mRNAs and increase expression of
proteins from downstream genes. The resulting recombinant viruses
will preferably exhibit increased growth kinetics and increased
plaque size, providing but one example of alteration of RSV
phenotype by changing cis-acting regulatory elements in the genome
or antigenome. These and other examples herein demonstrate a wide
range of RSV mutations specific for phenotypic changes that are
advantageous for providing effective vaccine agents.
EXAMPLE XVII
Recombinant RSV Having a Deletion of the NS1 Gene
This example describes the production of a recombinant RSV in which
expression of the NS1 protein has been ablated by removal of the
polynucleotide sequence encoding the protein. The NS1 protein is a
small 139-amino acid species which is encoded by the first gene in
the 3' to 5' RSV gene map (Collins and Wertz, Proc. Natl. Acad.
Sci. USA 80:3208-3212 (1983), and Collins and Wertz, Virol.
243:442-451 (1985)). Its mRNA is the most abundant of the RSV
mRNAs, consistent with the general finding that there is a gradient
of transcription such that the efficiency of gene expression is
reduced with increasing distance from the promoter at the 3' end.
The NS1 protein is thought to be one of the most abundantly
expressed RSV proteins, although a careful quantitative comparison
remains to be done. Despite its abundance, the function of the NS1
protein has not yet been clearly identified. In the reconstituted
RSV minigenome system (Grosfeld et al., J. Virol. 69:5677-5686
(1995), Collins et al., Proc. Natl. Acad. Sci. USA 93:81-85
(1996)), in which transcription and RNA replication of a minigenome
is driven by viral proteins supplied by plasmids, the NS1 protein
appeared to be a negative regulatory protein for both transcription
and RNA replication. Thus, it might be a regulatory protein. It is
very possible that other functions exist which remain to be
identified. The NS1 protein does not have a known counterpart in
other paramyxoviruses. Without wishing to be bound by theory,
several functions of the NS1 protein may exist: (i) it may be a
viral regulatory factor as suggested above, (ii) it may be involved
in some other aspect of the viral growth cycle, (iii) it may
interact with the host cell, such as to prevent apoptosis, and (iv)
it may interact with the host immune system, such as to inhibit
aspects of the host defense system such as interferon production,
antigen processing or B or T cell functioning. All of these
potential activities of the NS1 protein may yield additional
advantages in RSV recombinant vaccines.
To produce a recombinant RSV having a selected disruption of NS1
gene function, the sequence encoding the NS1 protein was deleted in
its entirety from a parental RSV cDNA. In this exemplary deletion,
the substrate for the mutagenesis reaction was plasmid D13, which
was described hereinabove and contains the left hand end of the
complete antigenome cDNA including the T7 RNA promoter, the leader
region, and the NS1, NS2, N, P, M, and SH genes (sequence positions
1 to 4623). The mutagenesis was done by the method of Byrappa et
al. (Byrappa et al., Genome Res. 5:404-407 (1995)), in which
synthetic primers which incorporate the desired change are made to
face in opposite directions on the plasmid, which is then amplified
by PCR, ligated, and transformed into bacteria. The forward PCR
primer was GACACAACCCACAATGATAATACACCAC [SEQ ID NO:9] (the second
codon of the NS2 ORF is italicized), and the reverse PCR primer was
CATCTCTAACCAAGGGAGTTAAATTTAAGTGG [SEQ ID NO:10] (the complement to
the initiation codon of the NS2 ORF is italicized). D13 was used as
the template for PCR with a high-fidelity polymerase. The deletion
was made to span from immediately upstream of the AUG start site of
the NS1 ORF to immediately upstream of the AUG start site of the
NS2 ORF (FIG. 21). This resulted in the deletion of 529 bp
including the NS1 coding sequence, the NS1 GE signal, the NS1-NS2
intergenic region, and the NS2 GS signal. It had the effect of
fusing the upstream end of the NS1 gene, namely its GS and
non-protein-coding region, to the NS2 ORF. This part of the NS1
gene was retained expressly because it is immediately adjacent to
the leader region and thus might contain sequences important in
transcription or RNA replication. The region containing the
mutation was confirmed by sequence analysis. Then, the .about.2230
bp segment between the Aat2 and Avr2 sites (FIG. 21) was excised
and inserted into a fresh copy of D13, a step that would thereby
preclude the possibility of PCR error elsewhere in the RSV cDNA.
The D13 plasmid containing the deletion of NS1 (D13_NS1) was used
to construct a complete antigenome (D53_NS1) which contained the
"HEK" and "sites" changes.
The D53_NS1 plasmid was then used to recover virus. Interestingly,
the recovered RSV_NS1 virus produced small plaques in tissue
culture. The presence of the deletion was confirmed by RT-PCR. The
fact that the RSV_NS1 virus can grow, albeit with reduced
efficiency, identifies the NS1 protein as an accessory protein, one
that is dispensable to virus growth. The plaque size of the RSV_NS1
virus was similar to that of the NS2-knock out virus described
above in which expression of the NS2 protein was ablated by the
introduction of translational stop codons into its coding sequence
(Example XV). The small plaque phenotype is commonly associated
with attenuating mutations. This type of mutation can thus be
incorporated within viable recombinant RSV to yield altered
phenotypes. These and other knock-out methods and mutants will
therefore provide for yet additional recombinant RSV vaccine
agents, based on the known correlation between plaque size in vitro
and attenuation in vivo.
EXAMPLE XVIII
Recombinant RSV Having a Deletion of the NS2 Gene
This example describes the production of a recombinant RSV in which
expression of the NS2 protein has been ablated by removal of a
polynucleotide sequence encoding the protein. In Example XV, above,
a recombinant virus (called NS2 knock-out or NS2-KO) was produced
in which expression of the NS2 gene was ablated by the introduction
of two translational stop codons into its coding sequence rather
than by deletion of the coding sequence. Ablation of expression of
the NS2 protein in the prototypic NS2-KO virus was associated with
the small plaque phenotype and reduced kinetics of virus growth in
vitro. Subsequent analysis showed that, upon passage of NS2 KO, it
was possible to recover low levels of virus which had reverted to
wild-type growth characteristics. Sequence analysis showed that the
two introduced translational stop codons had mutated into sense
codons, albeit with coding assignments different than in the
parental wild-type virus. This was sufficient to restore synthesis
of the NS2 protein as confirmed by Western blot analysis, which
accounted for the wild-type phenotype. The present strategy offers
an improvement because the complete NS2 gene is removed and thus
same-site reversion cannot occur.
The NS2 protein is a small 124-amino acid protein which is encoded
by the second gene in the gene order (Collins and Wertz, Proc.
Natl. Acad. Sci. USA 80:3208-3212 (1983), and Collins and Wertz,
Virol. 243:442 451 (1985). Its mRNA is the second most abundant of
the RSV mRNAs, and the NS2 protein is thought to be one of the most
abundantly-expressed RSV proteins, although a careful quantitative
comparison remains to be done. Despite its abundance, the function
of the NS2 protein remains to be identified. In the reconstituted
RSV minigenome system (Grosfeld et al., J. Virol. 69:5677-5686
(1995), Collins et al., Proc. Natl. Acad. Sci. USA 93:81-85
(1996)), in which transcription and RNA replication of a minigenome
is driven by viral proteins supplied by plasmids, the NS2 protein
had a modest negative regulatory effect against both transcription
and RNA replication. Relatively high levels of NS2 protein
expression were required to observe this effect, and so its
significance is unclear. Thus, as suggested for the NS1 protein,
NS2 might: (i) be a viral regulatory factor, (ii) be involved in
some other aspect of the viral growth cycle, (iii) interact with
the host cell, such as to prevent apoptosis, and (iv) interact with
the host defense system, such as to inhibit aspects of the host
immune system such as interferon production or aspects of antigen
processing or B or T cell functioning. All of these potential
activities of the NS2 protein may be incorporated within the
invention according to the methods and strategies described herein,
to yield additional advantages in RSV recombinant vaccines.
To produce a recombinant RSV having a selected disruption of NS2
gene function, the sequence encoding its mRNA was deleted from a
parental RSV cDNA. In this exemplary deletion, the substrate for
the mutagenesis reaction was plasmid D13, which was mentioned
previously and contains the left hand end of the complete
antigenome cDNA including the T7 RNA promoter, the leader region,
and the NS1, NS2, N, P, M, and SH genes (sequence positions 1 to
4623). The mutagenesis was done by the method of Byrappa et al.
(Byrappa et al., Genome Res. 5:404-407 (1995)), in which synthetic
primers which incorporate the desired change are made to face in
opposite directions on the plasmid, which is then amplified by PCR,
ligated, and transformed into bacteria. The forward PCR primer was
TTAAGGAGAGATATAAGATAGAAGATG [SEQ ID NO:11] (sequence from the NS2 N
intergenic region is underlined, and the first nucleotide of the N
GS signal is italicized), and the reverse PCR primer was
GTTTTATATTAACTAATGGTGTTAGTG [SEQ ID NO:12] (the complement to the
NS1 GE signal is underlined). D13 was used as the template for PCR
with a high-fidelity polymerase. The deletion was made to span from
immediately downstream of the NS1 GE signal to immediately
downstream of the NS2 GS signal (FIG. 22). Thus, the mutation
deleted 522 nucleotides including the NS1--NS2 intergenic region
and the complete NS2 gene (FIG. 22).
In the D13 plasmid containing the deletion, the region of the
mutation was confirmed by sequence analysis. Then, the .about.2230
bp segment between the Aat2 and Avr2 sites (FIG. 22) was excised
and inserted into a fresh copy of D13, a step that would thereby
preclude the possibility of PCR error elsewhere in the RSV cDNA.
The D13 plasmid containing the deletion of NS2 (D13_NS2) was used
to construct a complete antigenome (D53_NS2) which contained all of
the "sites" and "HEK" changes.
The D53_NS2 plasmid was then used to recover virus. As is described
above for the NS2-KO virus (see Example XV), the RSV_NS2 produced
small plaques. The presence of the deletion was confirmed by
RT-PCR. The fact that the RSV_NS2 virus can grow, albeit with
reduced efficiency, identified the NS2 protein as an accessory
protein, one that is dispensable to virus growth. The small plaque
phenotype is commonly associated with attenuating mutations and can
thus be incorporated within viable recombinant RSV to yield altered
phenotypes. In accordance with these findings, the NS2-minus mutant
exhibited a moderately attenuated phenotype in the upper
respiratory tract and a highly attenuated phenotype in the lower
respiratory tract in naive chimpanzees. This mutant also elicited
greatly reduced disease symptoms in chimps while stimulating
significant resistance to challenge by the wild-type virus.
Whitehead et al., J. Virol. 73:(4)3438-3442 (1999), incorporated
herein by reference. Therefore, these and other knock-out methods
and mutants will provide for yet additional recombinant RSV vaccine
agents, based on the known correlation between plaque size in vitro
and attenuation in vivo.
EXAMPLE XIX
Ablation of the Translational Start Site for the Secreted Form of
the G Glycoprotein
This example describes the production of a recombinant RSV in which
the translational start site for the secreted form of the G
glycoprotein has been ablated. The RSV G protein is synthesized in
two forms: as an anchored type II integral membrane protein and as
a N terminally resected form which lacks essentially all of the
membrane anchor and is secreted (Hendricks et al., J. Virol.
62:2228-2233 (1988)). The two forms have been shown to be derived
by translational initiation at two different start sites: the
longer form initiates at the first AUG of the G ORF, and the second
initiates at the second AUG of the ORF at codon 48 and is further
processed by proteolysis (Roberts et al., J. Virol. 68: 4538-4546
(1994)). The presence of this second start site is highly
conserved, being present in all strains of human, bovine and ovine
RSV sequenced to date. It has been suggested that the soluble form
of the G protein might mitigate host immunity by acting as a decoy
to trap neutralizing antibodies. Also, soluble G has been
implicated in preferential stimulation of a Th2-biased response,
which in turn appears to be associated with enhanced
immunopathology upon subsequent exposure to RSV. With regard to an
RSV vaccine virus, it would be highly desirable to minimize
antibody trapping or imbalanced stimulation of the immune system,
and so it would be desirable to ablate expression of the secreted
form of the G protein. This would represent a type of mutation
whose action would be to qualitatively and/or quantitatively alter
the host immune response, rather than to directly attenuate the
virus.
Plasmid pUC19 bearing the G, F and M2 genes (see Example VII) was
used as template in PCR mutagenesis by the procedure of Byrappa et
al. (Byrappa et al., Genome Res. 5:404-407 (1995). The forward PCR
primer was: TTATAATTGCAGCCATCATATTCATAGCCTCGG [SEQ ID NO:13], and
the reverse primer was: GTGAAGTTGAGATTACAATTGCCAGAATGG [SEQ ID NO:
14] (the complement of the two nucleotide changes is underlined).
This resulted in two amino acid coding changes (see FIG. 23),
namely AUG-48 to AUU-48, which ablates the translational start
site, and AUA-49 to GUA-49, which contributes to the insertion of
an MfeI site for the purpose of monitoring the mutation.
The sequence surrounding the site of mutation was confirmed by
dideoxynucleotide sequencing. Then, the PacI-StuI fragment, which
contains the G gene, was substituted into plasmid D50, which is
described hereinabove and contains the first nine genes from the
leader to the beginning of the L gene. This was then used to
construct a complete antigenome cDNA, D53/GM48I, which was used to
recover virus. These mutations have previously been shown to ablate
the expression of the secreted form of G under conditions where the
G cDNA was expressed in isolation from the other RSV genes by a
recombinant vaccinia virus (Roberts et al., J. Virol. 68:4538-4546
(1994)).
Two isolates of the recovered D53/M48I virus were evaluated for
growth kinetics in vitro in parallel with wild-type recombinant RSV
(FIG. 24). This showed that both viruses grew somewhat more slowly,
and to somewhat lower titers, than did the wild-type. This
difference in growth might be due to the reduced expression of the
G protein, which would be expected to occur since the AUG-48 of the
secreted form was eliminated whereas in this Example the AUG-1 of
the membrane-bound form was not modified to increase its
expression. In nature, the expression of AUG-1 of the G ORF is
thought to be suboptimal because it is preceded in the G sequence
by another AUG in another reading frame which opens a short ORF
that overlaps AUG-1 of the G ORF and thus would reduce its
expression. It might be anticipated that additional modification of
the antigenome cDNA to eliminate this ORF might restore full growth
properties. Alternatively, the mutations at position 48 and 49,
acting alone or in concert, might be deleterious to the function of
the G protein. The amino acid at position 49 could be restored to
its natural coding assignment, and a different amino acid
substitution could be chosen at position 48, which might restore
full growth properties. These possibilities can be readily
evaluated with the methods and materials described here.
Nonetheless, the recovery of the D53/GM48I virus shows that the
translational start site for the secreted form can be ablated, and
this virus is now available for evaluation in experimental animals
and humans.
EXAMPLE XX
Production of An Attenuated Chimeric RSV Vaccine Virus For RSV
Subgroup B
The present example describes the production of live-attenuated
chimeric vaccines specific to subgroup B RSV. The preceeding
examples demonstrate production of various, RSV subgroup A
live-attenuated vaccines having a range of selectable attenuating
mutations, including mutations adopted from biologically derived
mutants as well as a series of other defined nucleotide changes
within the RSV A genome. Each of these changes are amenable to
introduction, individually or in a full array of combinations, into
the full-length cDNA clone, and the phenotype of each recovered
recombinant virus can be readily characterized and confirmed to
confer a desired level of attenuation for vaccine use.
A live-attenuated RSV vaccine ideally should be effective against
multiple RSV strains and/or subgroups. In this regard, RSV is
considered to be serologically monotypic, since convalescent serum
against any one strain will neutralize other strains. However, it
has long been recognized that the efficiency of
cross-neutralization varies among different strains (Coates,
Alling, and Chanock, 1966). More recently, studies with monoclonal
antibodies and by sequence analysis showed that RSV strains can be
segregated into two antigenic subgroups, A and B (Anderson et al.,
J. Infect. Dis. 151(4):626-33 (1985); Collins et al., J. Gen.
Virol. 71(Pt 7):1571-6. (1990); Johnson et al., Proc. Natl. Acad.
Sci. USA 84(16):5625-9 (1987b); Mufson et al., J. Gen. Virol. 66(Pt
10):2111-24 (1985).
Sequence divergence between the RSV A and B subgroups exists across
the entire genome, but the extent of divergence is not uniform. The
two most divergent regions are the extracellular domains of the G
and SH proteins which, at the amino acid level, are 56 and 50%
divergent, respectively (Collins et al., J. Gen. Virol. 71(Pt
7):1571-6. (1990); Johnson et al., J. Gen. Virol. 69(Pt 10):2623-8
(1988); Johnson et al., Proc. Natl. Acad. Sci. USA 84(16): 5625-9
(1987b), each incorporated herein by reference. The F glycoprotein,
the third RSV transmembrane surface protein, is 11% different
between subgroups at the amino acid level (Johnson et al., J. Gen.
Virol. 69(Pt 10):2623-8 (1988)). The percent antigenic relatedness
between the two subgroups for the G and F proteins, which are the
two major protective antigens, was measured to be 5% and 50%,
respectively (Johnson et al., J. Virol. 61(10):3163-6 (1987a)).
This amount of difference is such that both antigenic subgroups
should be represented in an RSV vaccine, especially the G
glycoprotein.
For subgroup B, a comparable panel of attenuated vaccine candidates
or a collection of cDNA reagents from which to produce virus is not
yet available. However, an initial group of live-attenuated
subgroup B vaccine candidates has been prepared (Crowe et al., J.
Infect. Dis. 173(4), 829-39 (1996a)). While these candidates may be
unsatisfactory for vaccine use due to spontaneous deletion of the
SH and G genes (Karron et al., Proc. Natl. Acad. Sci. USA
94(25):13961-6 (1997a)), they will provided useful mutations for
use within chimeric RSV of the invention.
The present example provides a RSV subgroup B-specific vaccine
virus in which an attenuated subgroup A virus is used to express
the F and G glycoproteins of a subgroup B RSV. Because the F and G
proteins are the major protective antigens and confer most of the
RSV subgroup specificity, this chimeric virus will stimulate a
strong immune response against subgroup B. This strategy may be
implemented using two alternative approaches. One is to insert the
G glycoprotein gene of a subgroup B virus into the subgroup A
background as an additional gene. This virus would therefore encode
two G proteins, one of subgroup A and one of subgroup B. In this
context, Jin et al., Virology 251(1):206-14 (1998) described a
subgroup A virus which expresses the G protein of subgroup B as an
additional gene (Jin et al., Virology 251(1):206-14 (1998)).
However, since the F protein also exhibits significant
subgroup-specificity, it would be preferable to express both
subgroup B glycoproteins in a subgroup B-specific vaccine.
Moreover, it is desireable to further modify a subgroup B virus to
achieve proper attenuation and immunogenicity in accordance with
the teachings herein.
The second, more desirable strategy to achieve an RSV subgroup B
vaccine is disclosed in the present example, which documents
removal of the G and F genes from a subgroup A recombinant cDNA
backbone, and replaces them with the G and F genes of a subgroup B
RSV. Thus, a chimeric RSV is provided which contains the internal
proteins of subgroup A and the external protective antigens of
subgroup B. This virus can then be attenuated to a desired level
according to the methods of the invention by systematic
incorporation of attenuating mutations from those identified above
into a subgroup A background. This attenuated virus bearing the
subgroup B protective antigens can then be combined with a
biologically-derived or recombinant attenuated subgroup A virus to
yield a two-component RSV vaccine which would cover both antigenic
subgroups.
According to the general methods disclosed herein, a genomic or
antigenomic cDNA of a viral strain representing one subgroup, for
example RSV subgroup A, is modified so that the F and G surface
glycoprotein genes are replaced by their counterparts from a virus
of the heterologous subgroup, in this example RSV subgroup B. This
cDNA is then used to produce an infectious chimeric virus by the
above described methods involving transfection of cultured cells
with the antigenome or genome cDNA supported by plasmids expressing
RSV nucleocapsid and polymerase proteins (see also, Collins et al.,
Proc. Natl. Acad. Sci. USA 92:11563-11567 (1995); U.S. Provisional
Patent Application No. 60/007,083, each incorporated herein by
reference). Since the resulting virus bears the heterologous
subgroup F and G glycoproteins, which are the major protective
antigens, it will induce immunity that is highly effective against
subsequent infection by a virus of the heterologous subgroup.
Within the present example, any RSV glycoprotein or other relevant
gene or gene segment can be substituted singly. However, in the
case of protective antigens, the protective effect against a
heterologous subgroup virus is far more desirable if two or more
immunogenic proteins or epitopes are represented (either by
introduction of entire proteins or immunogenic regions thereof).
Other genes can also be substituted or included as additional
genes. For example, the gene encoding the third RSV surface
glycoprotein, SH, can also be substituted by its heterologous
subgroup counterpart, or added as a supernumary glycoprotein within
a chimeric RSV (see, e.g., Bukreyev et al., J. Virol.
71(12):8973-82 (1997), incorporated herein by reference). The
sequence replacements can involve any of the RSV genes or genetic
elements singly or in combination. For example, they can involve
substitution of part of a translational open reading frame (ORF), a
complete ORF, a complete gene including transcription signals,
cis-acting elements, or any combination or functional segments
thereof. In the present example, the transferred genes are placed
in the same genome locations which were occupied by their recipient
counterparts, but this need not be the case. For example, the donor
genes can be moved closer to or more distant from the viral
promoter in order to increase or decrease expression.
In practicing the current aspect of the invention, either subgroup
A or B RSV can be used as the recipient, with the other group
serving as the donor. In the examples described here, a subgroup A
backbone is the recipient for subgroup B glycoprotein genes. Also,
any subgroup A or B strain can be used, although the specific
examples described here involve the A2 and B1 strains. Additional
subgroups or significant antigenic variants might emerge in the
future, and could also readily provide useful recipient and/or
donor sequences for gene or gene segment exchanges and
transfers.
In conjunction with the present example, modification of the RSV
cDNA is further undertaken to render the cDNA capable of being
manipulated and propagated with maximum stability, if this is found
to be necessary. Instability in RSV sequences is common, and is
thought to be manifest during propagation in bacteria. However,
instability of RSV sequence also has been observed during passage
of the virus in cell culture. Specifically, the G gene of a
biologically-derived cpRSV of subgroup B was deleted during passage
in vero cells. In this example, the gene-end signal of the strain
B1 G gene was determined by routine methods to be unstable.
Altering the sequence in ways which did not alter amino acid coding
or greatly perturb cis-acting signals resulted in cDNA which could
be successfully propagated without unplanned changes.
A third aspect of the strategy described and validated in the
present example is that the backbone of a chimeric RSV can be
modified as necessary by introducing attenuating mutations in
selected combinations. For example, a strain A2 backbone can be
modified by the introduction of the cp mutations, ts mutations, and
various other mutations which have been characterized above to
yield desired functional or phenotypic characteristics, e.g., to
improve attenuation of the virus. These mutations can involve any
substitution, insertion, deletion or rearrangement which confers
the desirable property in this context. For example, deletion of
the SH gene has the additional property of larger plaque size and
improved growth in some cell lines. Other desirable properties
include, but are not limited to, improved antigen expression,
reduced reactogenicity, and improved or altered immunogenicity.
Importantly, the ability to introduce these mutations in stepwise
fashion and in various combinations renders it possible to achieve
a finely tuned balance between attenuation and immunogenicity, as
well as other desirable properties.
As the present example indicates, recombinant chimeric A/B virus
exhibits growth characteristics in cell culture and chimpanzees
which are wild-type-like and are intermediate between those
observed for parent strains A2 and B1. This shows that a fully
viable chimeric virus can readily be produced and further
manipulated to achieve desired changes. The property of
unrestricted growth in cell culture is crucial for the production
of vaccine virus. Also, a fully viable, wild-type-like virus is the
most appropriate substrate for subsequent attenuation in a directed
manner. Furthermore, since the growth properties of a chimeric A/B
virus are not very different than those of the A2 parent, the
introduction of desirable mutations which have been identified for
strain A2 are predicted to have similar effects in the AB
chimera.
As further described below, a panel of six A/B chimeric viruses
were developed in accordance with the methods of the invention,
which were modified by insertion of various combinations of known
attenuating mutations into the A2 RSV background. These examples
evince that many other modifications to the chimeric A/B virus
disclosed herein can be readily achieved to develop additional
vaccine strains. As expected, the A/B chimeric virus derivatives
showed phenotypes in cell culture which were consistent with those
of the corresponding recombinant attenuated strain A2 vaccine
candidates, indicating that the attenuation phenotypes are
reasonably predictable when transferred from a parent strain to a
chimeric derivative. For example, deletion of the SH gene in three
of the viruses resulted in an increase in plaque size, whereas the
addition of the 1030 mutation to two of the viruses resulted in
decreased plaque size which is consistent with attenuation. It
might be anticipated that some combinations of changes might yield
results that are not in complete accord with predictions.
Nonetheless, this invention provides the means for incremental
adjustments.
In the present example, RSV strain A2 is used as a donor in view of
the wide range of vaccine candidates and known phenotype-specific
mutations identified above. In this context, the description below
details the importation of representative attenuating mutations
which are placed into a chimeric recipient background, although in
practice they also can also be introduced into the donor gene(s).
The specific attenuating mutations described include: (i) three of
the five cp mutations, namely the mutation in N (V267I) and the two
in L (C319Y and H1690Y), but not the two in F since these are
removed by substitution with the B1 F gene; (ii) the 248 (Q831L),
1030 (Y1321N) and, optionally, 404-L (D1183E) mutations which have
been identified in attenuated strain A2 viruses; (iii) the single
nucleotide substitution at position 9 in the gene-start signal of
the M2 gene, and (iv) deletion of the SH gene. Other immediately
available mutations can include, but are not limited to, the NS1 or
NS2 gene deletions, or the 530 or 1009 mutations, alone or in
combination.
It is not uncommon for RSV cDNAs to sustain unwanted sequence
changes during manipulation or propagation in bacteria. For
example, the first strain A2 antigenome cDNA which was successfully
used to produce recombinant RSV exhibited separate instability
problems in the M and SH genes which were ameliorated by using a
lower-copy-number plasmid, growth at 30.degree. C. rather than
37.degree. C., and different bacterial strains (Collins et al.,
1995)). The G gene is also frequently associated with instability.
Furthermore, the RSV G gene has been shown to be unstable under
certain conditions of RSV growth in cell culture (Kerran et al.,
1992). To resolve this problem, stabilization of the sequence of
the strain B1 G gene was achieved by altering the nucleotide
sequence in a way designed to leave amino acid coding unchanged.
Although the changes altered cis-acting signals, this alteration
should not significantly alter function. These modifications
rendered the cDNA capable of being manipulated and propagated
without unplanned changes.
Construction and Recovery of a "Wild-Type" Chimeric AB Virus
As noted above, one of the available strategies for developing an
effective RSV subgroup B vaccine based on an attenuated RSV
subgroup A virus is to replace the G and F genes in the strain A2
antigenomic cDNA with a restriction fragment bearing the G and F
genes of subgroup B (FIG. 25A-C). The A2 antigenomic cDNA has a
naturally-occurring PacI site within the SH gene-end signal, and
during the construction of the antigenomic cDNA we had inserted an
SphI site in the F-M2 intergenic region (Collins et al., 1995).
Therefore, the cDNA fragment bearing the G and F genes of strain A2
could be replaced with a cDNA bearing the G and F genes of a
subgroup B donor strain, such strain as B1. If appropriate PacI and
SphI sites did not occur in the subgroup B strain, as was the case
with strain B1, they could be generated during PCR using mutagenic
oligonucleotides following standard procedures.
The B1 virus has been sequenced in its entirety by analysis of
RT-PCR products, which thus provides a consensus sequence, and was
shown to be a wt virus based on studies with human volunteers
(Karron et al., 1997a, incorporated herein by reference). The B1
virus was grown in HEp-2 cell culture and concentrated from the
clarified medium by precipitation with polyethylene glycol. The
virion RNA was extracted and purified (Collins et al., 1995) and
used as template for reverse transcription (RT) using random
hexamer primers by conventional procedures (Collins et al., 1995)
The resulting cDNA was subjected to the polymerase chain reaction
(PCR) to amplify the two genes in a single cDNA. The PCR was
performed with a positive-sense oligonucleotide designed to prime
at the beginning of the intergenic region preceding the G gene
(GCATGGATCCTTAATTAAAAATTAACATAATGATGAATTATTAGTATG [SEQ ID NO: 15];
annotated so that the PacI site is in bold italics, a BamHI site
used for cloning the initial PCR product is in italics, and the
subgroup B-specific sequence is underlined) and a negative-sense
primer which hybridized midway through the intergenic region on the
downstream side of the F gene
(GTGTTGGATCCTGATTGCATGCTTGAGGTTTTTATGTAACTATGAGTTAAG [SEQ ID NO:
16]; annotated as above, except that the SphI site is in bold
italics). The primers were designed to introduce a PacI site at the
upstream end of the intergenic region preceeding G and an SphI site
into the intergenic region that follows the F gene. The PacI and
SphI sites were flanked in turn each by BamHI sites for the
purposes of cloning the initial PCR product into the BamHI site of
pBR322.
Four cloned G-F cDNAs were analyzed completely by nucleotide
sequencing. Each of the cDNA clones was found to contain a similar
error in the G gene-end signal. This signal (AGTTATTCAAAAA [SEQ ID
NO: 17]) ends with a run of five A residues, but in each clone this
had been elongated to 30 or more. In addition, each cDNA contained
at least one additional mutation elsewhere in the G or F gene.
These errors might have been introduced by the RSV polymerase, RT,
the DNA polymerase used in PCR, or propagation in bacteria. By the
exchange of restriction fragments it was possible to eliminate all
of these differences except for the gene-end mutation. Additional
cloned DNAs were examined in this region, and each was found to
contain an elongated GE signal. A single cDNA clone was identified
which contained a GE signal of the correct sequence, but upon
further propagation in bacteria this too became elongated. This
suggested that the elongation occurred during propagation in
bacteria. Growth at a lower temperature and using other bacterial
strains failed to provide clones with the correct sequence at this
signal.
It is not uncommon for certain sequences to be difficult to
propagate stably in bacteria, for reasons which often are not
apparent from examination of the DNA sequence. For example, two
specific regions of the strain A2 antigenome cDNA are unstable
unless specific bacteria strains and growth conditions are used.
Because changes in bacterial strain and growth conditions failed to
stabilize the B1 cDNA, its sequence was modified to make it more
stable. To achieve this objective, a number of nucleotides at the
downstream end of the G gene and in the downstream intergenic
region were changed as follows: (i) for the last eleven codons of
the G ORF, the nucleotide assignment of the third nucleotide in
each codon was changed without altering the amino acid coding
assignment; (ii) the termination codon of the G ORF was changed to
an alternative termination codon assignment, (iii) four nucleotides
were introduced into the downstream nontranslated region of the G
gene between the ORF and the gene-end signal, (iv) the G gene-end
signal was changed by two nucleotide substitutions and the A tract
was reduced in length by one nucleotide, so that the signal became
identical to that of the F gene of strain A2, and (v) the G-F
intergenic region was shortened by 47 nucleotides and an MfeI site
was introduced (see FIG. 26).
Mutagenesis was conducted using a PCR-based procedure in which two
abutting oligonucleotides which contain the desired changes are
used to prime DNA synthesis in opposite directions on the plasmid
template, after which the resulting linear DNA is circularized by
ligation (Byrappa, Gavin, and Gupta, 1995). The positive-sense
oligonucleotide was as follows (broken into triplets at coding
nucleotides, with nucleotide assignments which differ from the wt
B1 sequence underlined, the introduced MfeI site in bold, and the G
gene end and F gene-start signals in italics):
TABLE-US-00044 C CAC GCC TAATGAGTTATATAAAACAATT GGGCAAATAACC ATG
GAG [SEQ ID NO: 18]
The negative-sense oligonucleotide was as follows (annotated as
described above):
TABLE-US-00045 GA CTG AGT GTT CTG AGT AGA GTT GGA TGT AGA GGG CTC
GGA TGC TG [SEQ ID NO: 19]
The G-F cDNA described above was used as template in a PCR using
the two oligonucleotide primers indicated above. The PCR product
was gel-purified, circularized by ligation, and cloned in E. coli
strain DH10B (Life Technologies). Six cloned cDNAs were identified
which were the appropriate size to contain the full-length insert,
and sequence analysis of the region containing the gene-end signal
showed that each of the six contained the correct sequence. One
cDNA, MH5-7, was sequenced in full and contained the correct
sequence. Its PacI-SphI fragment containing the subgroup B G and F
genes was then excised in preparation for the construction of a
chimeric antigenomic cDNA.
The antigenomic strain A2 cDNA D53 contained the following
features. First, it contained a G to C (negative-sense)
substitution at leader position 4, called the 4C mutation, as
described previously (Collins et al., 1995). This change has been
described in certain biologically-derived attenuated strains of RSV
but is not associated with an attenuation phenotype. However, it
has been described as an up-regulator of RNA replication (Grosfeld,
Hill, and Collins, 1995), and also improves the efficiency of
recovery of infectious virus from cDNA although it does not appear
to affect viral yield in cell culture (Collins et al., 1995).
Second, D53 contains five nucleotide substitutions and a single
nucleotide insertion which place restriction site markers in four
locations: immediately downsteam of the NS2 gene, upstream of the N
ORF, in between the G and F genes, and in between the F and M2
genes (Collins et al., 1995). The antigenomic cDNA also was then
further modified by the insertion of a set of six translationally
silent restriction site markers into the L gene, which are
collectively called the "sites" mutations (Whitehead et al.,
1998b).
It was undesirable to directly replace the PacI-SphI fragment of
the D53 cDNA with that bearing the B1 G and F genes because the
PacI and SphI sites are not unique in the D53 plasmid. Therefore,
this replacement was done on the subclone D50, which contains the
left-hand end of the antigenome cDNA from the 3' extragenic leader
region, through the first nine genes, and to the start of the L
gene (Collins et al., 1995; Whitehead et al., 1998b). In this D50
plasmid, the PacI and SphI sites are unique, and a direct
restriction fragment exchange was made. The remainder of the
antigenomic cDNA, namely the L gene and the trailer region and
adjoining T7 promoter, was contained in the plasmid D39sites, and
this cDNA was then inserted as a BamHI-MluI fragment into the
BamHI-MluI window of B/D50.
The resulting complete chimeric antigenomic cDNA was then used to
produce virus by the above described method of complementation with
N, P, M2-1 and L proteins expressed from cotransfected plasmids.
This resulted in the recovery of the recombinant chimeric virus
rAB, containing the B1 G and F genes in the wt A2 background. This
novel virus was readily propagated in cell culture and formed
plaques which were similar in size to those of wt rA2. The level of
virus produced in cell culture were essentially identical to that
of the wild-type parents. Expression of the B1 G and F
glycoproteins, and the lack of expression of the A2 G and F
glycoproteins, was demonstrated by immunoperoxidase staining using
monoclonal antibodies which are specific to the G proteins of
subgroup B and A, respectively. The presence of the B1 genes in the
A2 backbone was confirmed by RT-PCR of RNA purified from rAB
virions using oligonucleotide primers specific for the B1 sequence.
In summary, a chimeric AB cDNA was constructed and successfully
used to recover an infectious AB chimeric virus which has
properties consistent with it being very similar to its parents in
viability.
Although direct replacement of the strain A2 G and F genes by their
strain B1 counterparts introduces B1-specific gene-start and
gene-end transcription signals into the A2 background, this is not
considered to be an important factor in light of the close
similarity between the two viruses in these signals. For example,
the gene-start signals of the G and F genes are exactly conserved
between the subgroups, and the gene-end signal of the F gene has a
single change (AGTTATATAAAA [SEQ ID NO: 20] for strain A2, with the
underlined position being C in strain B1). The gene-end signal of
the G gene has three changes (AGTTACTTAAAAA [SEQ ID NO: 21] in
positive sense for strain A2, with the three underlined positions
being TTC for strain B1), but as noted above it was modified to be
identical to that of the F gene of strain A2 and thus would be
fully compatible with the strain A2 polymerase. The junctions
between the B1 cDNA and the A2 backbone involved the SH-G and F-M2
intergenic regions. The length of the former did not change from 44
nucleotides: this is the same for both the A2 and B1 viruses, and
the PacI site was designed to maintain this spacing. The length of
the F-M2 intergenic region is 46 and 45 nucleotides for strains A2
and B1, respectively, and the AB chimera was designed to have the
latter length. The G-F intergenic region was reduced in length to 5
nucleotides as described above, which is much shorter than its
counterpart in the A2 and B1 viruses, which is 52 nucleotides in
each case. Moreover, even though the naturally-occurring intergenic
regions of RSV show considerable diversity in sequence and length
between gene junctions and between viruses, those of strain A2 are
equivalent with regard to their effect on minigenome replication
and transcription, and thus the changes introduced here into the
intergenic region likely will be silent (Kuo et al., 1996,
incorporated herein by reference).
Construction and Recovery of AB chimeric RSV Having Attenuating
Mutations in the A2 Backbone
In accordance with the general teachings of the invention, the
strain B1 G-F cDNA was substituted into a series of A2 backbones
which contained various combinations of attenuating mutations for
the purpose of generating attenuated AB viruses as vaccine
candidates for subgroup B. These attenuating mutations included:
(i) three of the five amino acid substitutions of cpRSV, namely the
mutation in N (V267I) and the two in L (C319Y and H1690Y), but not
the two in F since these are removed by substitution with the B1 F
gene; (ii) the 248 (Q831L), 1030 (Y1321N) and, optionally, 404-L
(D1183E) amino acid substitutions which were identified in the L
protein of the attenuated strain A2 viruses cpts248, cpts248/404,
and cpts530/1030; (iii) the nucleotide substitution at position 9
of the gene-start signal of the M2 gene of cpts248/404, and (iv)
deletion of the SH gene. In the case of mutations in the L gene,
these were inserted into the D39 plasmid containing the L gene as
described above, and then combined with B/D50 plasmid as described
above to make complete antigenomic cDNA. In the case of mutations
that lie within D50, restriction fragment substitution was used to
replace the relevant regions either within B/D50, which was then
joined with D39, or within B/D53. Each mutation was marked by the
introduction of a new restriction site, or ablation of a
naturally-occurring one, which was silent at the amino acid level,
as previously described (Juhasz et al., 1998; Juhasz et al., 1997;
Whitehead et al., 1998a; Whitehead et al., 1998b, each incorporated
herein by reference). In all cases, the structure of regions of
antigenomic cDNA which were modified by mutagenesis was confirmed
by nucleotide sequence analysis. A total of six modified AB
antigenomic cDNAs were made. Each antigenomic cDNA was then used to
recover infectious virus as described above, and in each case the
chimeric virus was successfully recovered. The presence of each
planned mutation in each recombinant virus was confirmed by reverse
transcription (RT)-polymerase chain reaction (PCR) followed by
restriction analysis or nucleotide sequencing. The six different
recombinant AB chimeras containing attenuating mutations which have
were recovered are listed in Table 44. Specifically, these
attenuated chimeras include rAB, which is a wild-type chimera
constructed with a wild-type strain A2 backbone and wild-type B1 G
and F genes. The remaining viruses contain a variety of attenuating
mutations in the strain A2 backbone and represent candidate
vaccines against subgroup B. Each virus can be propagated in cell
culture. This illustrates the feasibility of generating AB chimeras
containing a number of different combinations of mutations.
TABLE-US-00046 TABLE 44 RSV Subgroup B Vaccine Candidates Based on
Recombinant AB Chimeric Viruses Virus.sup.1 Description.sup.2 rAB
Wild type rABcp Cold passage (cp) mutations.sup.3 rAB.DELTA.SH
Deletion of SH gene rABcp248/404.DELTA.SH plus deletion of the SH
gene rABcp248/404/1030 (cp, 248.sup.4 and 404.sup.5 mutations) plus
the 1030.sup.6 mutation rABcp248/404/1030.DELTA.SH
rABcp248/404/1030 plus deletion of the SH gene .sup.1All viruses
are strain A2 in which the F and G glycoprotein genes have been
replaced with those of strain B1. .sup.2Phenotypes in cell culture
which are consistent with expected properties conferred by
mutations are as follows: each virus containing the .DELTA.SH
mutation made larger plaques than its counterpart containing the SH
gene, and each virus containing the 1030 mutation made smaller
plaques than its counterpart lacking the mutation. .sup.3The cp
mutations are the three amino acid substitutions in the N and L
proteins: the two substitutions in F are not involved due to the
gene replacement. .sup.4The 248 mutation is Gln-831-Leu in the L
protein. .sup.5The 404 mutations are Asp-1183-Glu in the L protein
and a point mutation in the M2 gene-start signal. .sup.6The 1030
mutation is Tyr-1321-Asn in the L protein.
Two of the introduced mutations would be expected to confer
phenotypes discernable in cell culture, based on their effect on
strain A2. For example, the introduction of the _SH mutant confers
larger plaque size, and the 1030 mutant confers reduced plaque
size. Each of the AB chimeras which contained these mutations
behaved appropriately. For example, the three chimeras lacking the
SH gene made plaques which were larger than those of the
corresponding virus which contained the SH gene. This suggests that
these chimeras will also possess the mild attenuation phenotype
which is associated with the deletion. Also, the addition of the
1030 mutation to rABcp248/404 and rABcp248/404_SH resulted in a
decrease in plaque size compared to counterparts which lacked the
1030 mutation. This indicates that whenever a mutation was
introduced which was predicted to alter the cell culture phenotype,
the expected change was observed in the chimeric virus. It may be
that some combinations will not conform to predictions.
Nonetheless, this provides a method for incremental changes in
phenotype. It is likely that other phenotypes associated with these
mutations, such as attenuation in vivo, also will be conferred to
the AB chimeras.
In addition, as shown in Table 45, the following viruses were
analyzed for the temperature sensitive phenotype by measuring the
efficiency of plaquing at various temperatures: the
biologically-derived A2 and B1 wt viruses, the wt chimeric rAB
virus, and the following derivatives of rAB containing attenuating
mutations: rABcp, containing the cp mutations in N (V267I) and L
(C319Y and H1690Y); rAB.DELTA.SH, which is rAB from which the SH
gene had been deleted; rABcp.DELTA.SH, which contains the
aforementioned cp changes and SH deletion; rABcp248/404.DELTA.SH,
which is a version of rABcpASH which also contains the 248 (Q831L
in the L protein) and 404 (D1183E in the L protein and a point
mutation in the M2 gene start signal) mutations; and
rABcp248/404/1030, which is a version of rABcp which contains the
248 and 404 mutations together with the 1030 mutation (Y1321N in
the L protein). As shown in Table 45, the biologically-derived A2
and B1 viruses were not temperature sensitive. Viruses containing
the B glycoprotein replacements showed a slight sensitivity, with a
shut off temperature of 40 C. Inclusion of the cp and ASH mutations
had no effect, which was expected since these do not confer the ts
phenotype in strain A2. Inclusion of the 248 and 404 mutations
together, or the 248, 404 and 1030 mutations together, yielded
viruses with shut off temperatures of 37 C and 36 C, respectively,
with small plaques formed at the next lower temperature in each
case. These results are essentially indistinguishable from those
obtained with these same two constellations of mutations placed in
the wt A2 recombinant background. Thus, it has been possible to
faithfully reconstruct these ts phenotypes in the rAB chimeras.
TABLE-US-00047 TABLE 45 Temperature sensitivity of AB chimeric RSV
derivatives Virus titer (log.sub.10pfu/ml) on HEp-2 cells Shut- at
indicated temperature (.degree. C.) off Virus 32 35 36 37 38 39 40
temp..sup.a rABcp248/ 3.6 2.4* <0.7 <0.7 <0.7 <0.7
<0.7 36 404/1030 rABcp248/ 5.2 3.9 3.8* <0.7 <0.7 <0.7
<0.7 37 404.DELTA.SH rABcp.DELTA.SH 4.6 4.6 4.8 4.8 4.4 3.6*
<0.7 40 rAB.DELTA.SH 4.9 4.1 4.4 4.1 4.1 3.2* <0.7 40 rABcp
4.8 4.0 4.4 3.8 3.2 3.2* <0.7 40 rAB 4.5 4.3 4.1 4.2 3.1 3.7*
2.2 40 wt RSV A2 5.3 5.2 5.3 5.0 5.1 5.1 4.8 >40 wt RSV B1 4.9
4.9 5.0 4.6 4.4 3.8 3.2 >40 .sup.aShut-off temperature is
defined as the lowest restrictive temperature at which a 100-fold
or greater reduction of titer is observed. Virus titers at the
shut-off temperature are bolded. *Pin-point plaque size
Growth of rAB Viruses in the Respiratory Tract of Cotton Rats and
Chimpanzees
The chimeric recombinant rAB virus was evaluated for its ability to
grow in the respiratory tract of cotton rats, a widely accepted
model in which RSV A2 and B1 replicate comparably. Animals in
groups of 5-6 were inoculated intranasally with 10.sup.6 pfu per
animal of wt rAB virus or its _SH, cp or cp_SH derivatives. Since
the attenuation phenotype associated with the _SH mutation is
marginal in rodents, and that associated with the cp mutation set
is essentially undetectable in rodents due to its host range
nature, the purpose of this initial study was simply to demonstrate
viability in vivo. On day 4 post infection, nasal turbinates and
lungs were harvested and virus titers were determined by plaque
assay. The parental A2 and B1 viruses replicated to
10.sup.6.0-10.sup.6.5 pfu per g tissue. The wild type chimeric rAB
virus and its derivatives containing attenuating mutations
replicated to between 10.sup.2 and 10.sup.4 pfu g. This showed that
the wild type and mutant AB viruses were viable in an experimental
animal. also, it raises the possibility that the exchange of
glycoproteins in the chimera was itself an attenuating change,
although as shown below this appears to be a rodent-specific
effect.
The chimpanzee is the experimental animal which most closely
resembles the human with regard to RSV growth and disease.
Therefore the wt rAB chimeric virus was administered to four
seronegative juvenile chimpanzees, with each animal inoculated
intranasally and intratracheally with 10.sup.5 pfu in a one ml
inoculum at each site. An additional three animals were inoculated
in the same way with the putative attenuated derivative
rAPcp248/404/1030. Nasopharyngeal swabs were taken daily from day 1
to day 10 and on day 12, and tracheal lavages were taken on days 2,
5, 6, 8 and 12 (Table 46). For comparison, other animals received
at a dose of 10.sup.4 or 10.sup.5 plaque forming units (PFU)/site,
as indicated. The table gives data for each animal with regard to
shedding in the upper (nasopharyngeal swab) and lower (tracheal
lavage) respiratory tract from days 1 to 12, and the peak
rhinorrhea score on an increasing scale of 0 to 4. This also is
illustrated in FIG. 27. The rAB chimera replicated to average peak
titers of 4.3 log.sub.10 and 4.1 log.sub.10 pfu/ml in the
nasopharynx and trachea, respectively. This exceeded the levels of
replication of the biologically-derived wt B1 virus. Furthermore,
the rAB virus caused disease symptoms (rhinorrhea) which equalled
or exceeded the severity of those of the wt B1 virus. In contrast,
replication of the rABcp248/404/1030 virus was highly restricted.
This virus was not recovered from any of the tracheal lavages,
representing a reduction in replication of greater than 2,500-fold
whereas in the upper respiratory tract the rABcp248/404/1030 virus
replicated to a mean peak titer of 2.0 log.sub.10 pfu/ml, which was
200-fold lower than that of the rAB wt. There were no disease
symptoms associated with the rABcp248/404/1030 virus. These
findings illustrate that the introduction of attenuating mutations
into the A2 background restricts replication and eliminates disease
symptoms.
TABLE-US-00048 TABLE 46 Replication of recombinant chimeric virus
rAB in the upper and lower respiratory tract of chimpanzees Peak
Virus rhi- (log.sub.10 Nasopharyngeal swab titer (log.sub.10
pfu/ml) Tracheal lavage titer (log.sub.10pfu/ml) nor- pfu/ Day
post-inoculation Day post-inoculation rhea Chimp site).sup.a 1 2 3
4 5 6 7 8 9 10 12 Peak 2 5 6 8 12 Peak score 1622 rAB <0.7 0.7
3.0 3.6 3.7 3.9 4.1 2.2 0.7 <0.7 <0.7 4.1 <0- .7 3.7 4.1
2.0 <0.7 4.1 2 (5.0) 1625 rAB <0.7 1.2 3.0 2.7 3.7 4.2 4.6
2.5 1.7 <0.7 <0.7 4.6 <0- .7 3.7 3.4 2.6 <0.7 3.7 3
(5.0) 1627 rAB <0.7 1.7 2.9 2.9 4.1 3.7 4.3 2.3 1.7 <0.7
<0.7 4.3 <0- .7 4.5 3.8 2.5 <0.7 4.5 2 (5.0) 1628 rAB
<0.7 1.5 3.6 2.9 3.4 3.5 4.1 1.5 0.7 <0.7 <0.7 4.1 <0-
.7 3.2 3.9 2.5 <0.7 3.9 3 (5.0) mean 4.3 4.1 2.5 5835 wtB1
<0.7 <0.7 2.7 1.7 3.0 2.1 2.2 <0.7 <0.7 <0.7 <-
0.7 3.0 <0.7 <0.7 <0.7 <0.7 <0.7 1.0 1 (5.0) 5867
wtB1 <0.7 <0.7 2.3 2.5 1.8 2.4 1.9 2.2 <0.7 <0.7
<0.7 - 2.5 <0.7 3.9 <0.7 <0.7 <0.7 3.9 2 (5.0) mean
2.8 2.5 1.5 337 wtB1 <0.7 <0.7 2.4 2.9 2.9 2.9 3.7 1.0 2.5
<0.7 <0.7 3.7 &- lt;0.7 <0.7 <0.7 <0.7 <0.7
<0.7 3 (4.0) 346 wtB1 <0.7 <0.7 <0.7 <0.7 <0.7
2.7 3.0 2.2 2.7 2.9 <0- .7 3.0 <0.7 <0.7 <0.7 <0.7
<0.7 <0.7 2 (4.0) 362 wtB1 <0.7 <0.7 <0.7 <0.7
<0.7 <0.7 2.5 2.3 <0.7 1- .7 <0.7 2.5 <0.7 <0.7
<0.7 <0.7 <0.7 <0.7 3 (4.0) 365 wtB1 <0.7 <0.7
<0.7 1.0 1.4 2.2 2.2 2.7 <0.7 0.7 <0.7 2- .7 <0.7
<0.7 <0.7 3.4 <0.7 3.4 2 (4.0) mean 3.0 1.4 2.5 96A001
1030 <0.7 <0.7 <0.7 1.0 1.2 2.4 1.3 1.6 2.0 <0.7
<0.- 7 2.4 <0.7 <0.7 <0.7 <0.7 <0.7 <0.7 0
(5.0).sup.b 95A013 1030 <0.7 <0.7 <0.7 1.0 0.7 1.9 1.3 1.8
1.5 <0.7 <0.- 7 1.9 <0.7 <0.7 <0.7 <0.7 <0.7
<0.7 0 (5.0).sup.b 95a014 1030 <0.7 <0.7 1.0 1.0 1.0 1.6
1.8 1.8 1.0 1.0 <0.7 1.8 &l- t;0.7 <0.7 <0.7 <0.7
<0.7 <0.7 0 (5.0).sup.b mean 2.0 <0.7 0 .sup.aEach virus
was administered in a 1.0 ml inoculum intranasally and
intratracheally. .sup.bVirus administered was rABcp248/404/1030
To further evince successful practice of the invention, replication
of the wt rAB chimera was compared with that of the wt A2 virus.
Table 47 shows a summary of the data for the wt viruses from Table
46, together with historic controls involving two versions of
strain A2: (i) four animals which had received rA2 at a dose of
10.sup.4 pfu per site, and (ii) four which had received
biologically-derived A2 at a dose of 10.sup.4 pfu per site. This
comparison showed that the wt B1 virus replicated less efficiently
than did the wt A2 virus, whether biologically-derived or
recombinant. Furthermore, growth of the chimeric AB virus was
intermediate between that of the parental A2 and B1 viruses. The
intermediate nature of the growth of rAB compared to its parents
suggests that both the A2 backbone and the B1 glycoproteins
contribute to growth fitness. The poor growth of the rAB viruses in
cotton rats is likely attributed to a host range effect which
reduces fitness in rodents but not primates. The level of
replication in rodents can generally be used to predict the level
in chimpanzees and humans. However, some dissociation between
rodents and primates is occasionally observed, as in the present
case.
TABLE-US-00049 TABLE 47 rAB Chimpanzee Study Summary Mean peak
virus titer Mean Peak (log.sub.10 pfu/ml) Rhinorrhea Virus
Nasophar- Score (log.sub.10pfu/ No. of yngeal Tracheal (Range = No.
site) chimps Swab Lavage 0-4) 1 rAB (5.0) 4 4.3 .+-. 0.12 4.1 .+-.
0.17 2.5 2 wtB1 (5.0) 2 2.8 .+-. 0.25 2.5 .+-. 1.45 1.5 3 wtB1
(4.0) 4 3.0 .+-. 0.26 1.4 .+-. 0.68 2.5 4 rA2sites 4 5.0 .+-. 0.14
4.7 .+-. 0.43 2.5 (4.0) 5 wtA2 (4.0) 4 5.0 .+-. 0.35 5.5 .+-. 0.40
3.0
These foregoing results show that the G and F glycoproteins of a
subgroup A virus, in this example strain A2, can be replaced by
those of a subgroup B virus, in this example strain B1, without
compromising viability. The chimera was fully competent for
replication in the chimpanzee, the experimental animal which is the
most permissive and is the most reliable model for infection in
humans. Furthermore, the chimeric AB virus could be attenuated by
the introduction of known attenuating mutations into the strain A2
backbone.
Although the foregoing invention has been described in some detail
by way of illustration and example for purposes of clarity of
understanding, it will be obvious that certain changes and
modifications may be practiced within the scope of the appended
claims.
SEQUENCE LISTINGS
1
38115223DNARespiratory Syncytial Virus 1acgcgaaaaa atgcgtacaa
caaacttgca taaaccaaaa aaatggggca aataagaatt 60tgataagtac cacttaaatt
taactccctt ggttagagat gggcagcaat tcattgagta 120tgataaaagt
tagattacaa aatttgtttg acaatgatga agtagcattg ttaaaaataa
180catgctatac tgataaatta atacatttaa ctaatgcttt ggctaaggca
gtgatacata 240caatcaaatt gaatggcatt gtgtttgtgc atgttattac
aagtagtgat atttgcccta 300ataataatat tgtagtaaaa tccaatttca
caacaatgcc agtactacaa aatggaggtt 360atatatggga aatgatggaa
ttaacacatt gctctcaacc taatggtcta ctagatgaca 420attgtgaaat
taaattctcc aaaaaactaa gtgattcaac aatgaccaat tatatgaatc
480aattatctga attacttgga tttgatctta atccataaat tataattaat
atcaactagc 540aaatcaatgt cactaacacc attagttaat ataaaactta
acagaagaca aaaatggggc 600aaataaatca attcagccaa cccaaccatg
gacacaaccc acaatgataa tacaccacaa 660agactgatga tcacagacat
gagaccgttg tcacttgaga ccataataac atcactaacc 720agagacatca
taacacacaa atttatatac ttgataaatc atgaatgcat agtgagaaaa
780cttgatgaaa agcaggccac atttacattc ctggtcaact atgaaatgaa
actattacac 840aaagtaggaa gcactaaata taaaaaatat actgaataca
acacaaaata tggcactttc 900cctatgccaa tattcatcaa tcatgatggg
ttcttagaat gcattggcat taagcctaca 960aagcatactc ccataatata
caagtatgat ctcaatccat aaatttcaac acaatattca 1020cacaatctaa
aacaacaact ctatgcataa ctatactcca tagtccagat ggagcctgaa
1080aattatagta atttaaaact taaggagaga tataagatag aagatggggc
aaatacaacc 1140atggctctta gcaaagtcaa gttgaatgat acactcaaca
aagatcaact tctgtcatcc 1200agcaaataca ccatccaacg gagcacagga
gatagtattg atactcctaa ttatgatgtg 1260cagaaacaca tcaataagtt
atgtggcatg ttattaatca cagaagatgc taatcataaa 1320ttcactgggt
taataggtat gttatatgcg atgtctaggt taggaagaga agacaccata
1380aaaatactca gagatgcggg atatcatgta aaagcaaatg gagtagatgt
aacaacacat 1440cgtcaagaca ttaatggaaa agaaatgaaa tttgaagtgt
taacattggc aagcttaaca 1500actgaaattc aaatcaacat tgagatagaa
tctagaaaat cctacaaaaa aatgctaaaa 1560gaaatgggag aggtagctcc
agaatacagg catgactctc ctgattgtgg gatgataata 1620ttatgtatag
cagcattagt aataactaaa ttagcagcag gggacagatc tggtcttaca
1680gccgtgatta ggagagctaa taatgtccta aaaaatgaaa tgaaacgtta
caaaggctta 1740ctacccaagg acatagccaa cagcttctat gaagtgtttg
aaaaacatcc ccactttata 1800gatgtttttg ttcattttgg tatagcacaa
tcttctacca gaggtggcag tagagttgaa 1860gggatttttg caggattgtt
tatgaatgcc tatggtgcag ggcaagtgat gttacggtgg 1920ggagtcttag
caaaatcagt taaaaatatt atgttaggac atgctagtgt gcaagcagaa
1980atggaacaag ttgttgaggt ttatgaatat gcccaaaaat tgggtggtga
agcaggattc 2040taccatatat tgaacaaccc aaaagcatca ttattatctt
tgactcaatt tcctcacttc 2100tccagtgtag tattaggcaa tgctgctggc
ctaggcataa tgggagagta cagaggtaca 2160ccgaggaatc aagatctata
tgatgcagca aaggcatatg ctgaacaact caaagaaaat 2220ggtgtgatta
actacagtgt actagacttg acagcagaag aactagaggc tatcaaacat
2280cagcttaatc caaaagataa tgatgtagag ctttgagtta ataaaaaatg
gggcaaataa 2340atcatcatgg aaaagtttgc tcctgaattc catggagaag
atgcaaacaa cagggctact 2400aaattcctag aatcaataaa gggcaaattc
acatcaccca aagatcccaa gaaaaaagat 2460agtatcatat ctgtcaactc
aatagatata gaagtaacca aagaaagccc tataacatca 2520aattcaacta
ttatcaaccc aacaaatgag acagatgata ctgcagggaa caagcccaat
2580tatcaaagaa aacctctagt aagtttcaaa gaagacccta caccaagtga
taatcccttt 2640tctaaactat acaaagaaac catagaaaca tttgataaca
atgaagaaga atccagctat 2700tcatacgaag aaataaatga tcagacaaac
gataatataa cagcaagatt agataggatt 2760gatgaaaaat taagtgaaat
actaggaatg cttcacacat tagtagtggc aagtgcagga 2820cctacatctg
ctcgggatgg tataagagat gccatggttg gtttaagaga agaaatgata
2880gaaaaaatca gaactgaagc attaatgacc aatgacagat tagaagctat
ggcaagactc 2940aggaatgagg aaagtgaaaa gatggcaaaa gacacatcag
atgaagtgtc tctcaatcca 3000acatcagaga aattgaacaa cctattggaa
gggaatgata gtgacaatga tctatcactt 3060gaagatttct gattagttac
caatcttcac atcaacacac aataccaaca gaagaccaac 3120aaactaacca
acccaatcat ccaaccaaac atccatccgc caatcagcca aacagccaac
3180aaaacaacca gccaatccaa aactaaccac ccggaaaaaa tctataatat
agttacaaaa 3240aaaggaaagg gtggggcaaa tatggaaaca tacgtgaaca
agcttcacga aggctccaca 3300tacacagctg ctgttcaata caatgtctta
gaaaaagacg atgaccctgc atcacttaca 3360atatgggtgc ccatgttcca
atcatctatg ccagcagatt tacttataaa agaactagct 3420aatgtcaaca
tactagtgaa acaaatatcc acacccaagg gaccttcact aagagtcatg
3480ataaactcaa gaagtgcagt gctagcacaa atgcccagca aatttaccat
atgcgctaat 3540gtgtccttgg atgaaagaag caaactagca tatgatgtaa
ccacaccctg tgaaatcaag 3600gcatgtagtc taacatgcct aaaatcaaaa
aatatgttga ctacagttaa agatctcact 3660atgaagacac tcaaccctac
acatgatatt attgctttat gtgaatttga aaacatagta 3720acatcaaaaa
aagtcataat accaacatac ctaagatcca tcagtgtcag aaataaagat
3780ctgaacacac ttgaaaatat aacaaccact gaattcaaaa atgctatcac
aaatgcaaaa 3840atcatccctt actcaggatt actattagtc atcacagtga
ctgacaacaa aggagcattc 3900aaatacataa agccacaaag tcaattcata
gtagatcttg gagcttacct agaaaaagaa 3960agtatatatt atgttaccac
aaattggaag cacacagcta cacgatttgc aatcaaaccc 4020atggaagatt
aacctttttc ctctacatca gtgtgttaat tcatacaaac tttctaccta
4080cattcttcac ttcaccatca caatcacaaa cactctgtgg ttcaaccaat
caaacaaaac 4140ttatctgaag tcccagatca tcccaagtca ttgtttatca
gatctagtac tcaaataagt 4200taataaaaaa tatacacatg gggcaaataa
tcattggagg aaatccaact aatcacaata 4260tctgttaaca tagacaagtc
cacacaccat acagaatcaa ccaatggaaa atacatccat 4320aacaatagaa
ttctcaagca aattctggcc ttactttaca ctaatacaca tgatcacaac
4380aataatctct ttgctaatca taatctccat catgattgca atactaaaca
aactttgtga 4440atataacgta ttccataaca aaacctttga gttaccaaga
gctcgagtca acacatagca 4500ttcatcaatc caacagccca aaacagtaac
cttgcattta aaaatgaaca acccctacct 4560ctttacaaca cctcattaac
atcccaccat gcaaaccact atccatacta taaagtagtt 4620aattaaaaat
agtcataaca atgaactagg atatcaagac taacaataac attggggcaa
4680atgcaaacat gtccaaaaac aaggaccaac gcaccgctaa gacattagaa
aggacctggg 4740acactctcaa tcatttatta ttcatatcat cgtgcttata
taagttaaat cttaaatctg 4800tagcacaaat cacattatcc attctggcaa
tgataatctc aacttcactt ataattgcag 4860ccatcatatt catagcctcg
gcaaaccaca aagtcacacc aacaactgca atcatacaag 4920atgcaacaag
ccagatcaag aacacaaccc caacatacct cacccagaat cctcagcttg
4980gaatcagtcc ctctaatccg tctgaaatta catcacaaat caccaccata
ctagcttcaa 5040caacaccagg agtcaagtca accctgcaat ccacaacagt
caagaccaaa aacacaacaa 5100caactcaaac acaacccagc aagcccacca
caaaacaacg ccaaaacaaa ccaccaagca 5160aacccaataa tgattttcac
tttgaagtgt tcaactttgt accctgcagc atatgcagca 5220acaatccaac
ctgctgggct atctgcaaaa gaataccaaa caaaaaacca ggaaagaaaa
5280ccactaccaa gcccacaaaa aaaccaaccc tcaagacaac caaaaaagat
cccaaacctc 5340aaaccactaa atcaaaggaa gtacccacca ccaagcccac
agaagagcca accatcaaca 5400ccaccaaaac aaacatcata actacactac
tcacctccaa caccacagga aatccagaac 5460tcacaagtca aatggaaacc
ttccactcaa cttcctccga aggcaatcca agcccttctc 5520aagtctctac
aacatccgag tacccatcac aaccttcatc tccacccaac acaccacgcc
5580agtagttact taaaaacata ttatcacaaa aggccttgac caacttaaac
agaatcaaaa 5640taaactctgg ggcaaataac aatggagttg ctaatcctca
aagcaaatgc aattaccaca 5700atcctcactg cagtcacatt ttgttttgct
tctggtcaaa acatcactga agaattttat 5760caatcaacat gcagtgcagt
tagcaaaggc tatcttagtg ctctgagaac tggttggtat 5820accagtgtta
taactataga attaagtaat atcaagaaaa ataagtgtaa tggaacagat
5880gctaaggtaa aattgataaa acaagaatta gataaatata aaaatgctgt
aacagaattg 5940cagttgctca tgcaaagcac acaagcaaca aacaatcgag
ccagaagaga actaccaagg 6000tttatgaatt atacactcaa caatgccaaa
aaaaccaatg taacattaag caagaaaagg 6060aaaagaagat ttcttggttt
tttgttaggt gttggatctg caatcgccag tggcgttgct 6120gtatctaagg
tcctgcacct agaaggggaa gtgaacaaga tcaaaagtgc tctactatcc
6180acaaacaagg ctgtagtcag cttatcaaat ggagttagtg ttttaaccag
caaagtgtta 6240gacctcaaaa actatataga taaacaattg ttacctattg
tgaacaagca aagctgcagc 6300atatcaaata tagaaactgt gatagagttc
caacaaaaga acaacagact actagagatt 6360accagggaat ttagtgttaa
tgcaggcgta actacacctg taagcactta catgttaact 6420aatagtgaat
tattgtcatt aatcaatgat atgcctataa caaatgatca gaaaaagtta
6480atgtccaaca atgttcaaat agttagacag caaagttact ctatcatgtc
cataataaaa 6540gaggaagtct tagcatatgt agtacaatta ccactatatg
gtgttataga tacaccctgt 6600tggaaactac acacatcccc tctatgtaca
accaacacaa aagaagggtc caacatctgt 6660ttaacaagaa ctgacagagg
atggtactgt gacaatgcag gatcagtatc tttcttccca 6720caagctgaaa
catgtaaagt tcaatcaaat cgagtatttt gtgacacaat gaacagttta
6780acattaccaa gtgaagtaaa tctctgcaat gttgacatat tcaaccccaa
atatgattgt 6840aaaattatga cttcaaaaac agatgtaagc agctccgtta
tcacatctct aggagccatt 6900gtgtcatgct atggcaaaac taaatgtaca
gcatccaata aaaatcgtgg aatcataaag 6960acattttcta acgggtgcga
ttatgtatca aataaagggg tggacactgt gtctgtaggt 7020aacacattat
attatgtaaa taagcaagaa ggtaaaagtc tctatgtaaa aggtgaacca
7080ataataaatt tctatgaccc attagtattc ccctctgatg aatttgatgc
atcaatatct 7140caagtcaacg agaagattaa ccagagccta gcatttattc
gtaaatccga tgaattatta 7200cataatgtaa atgctggtaa atccaccaca
aatatcatga taactactat aattatagtg 7260attatagtaa tattgttatc
attaattgct gttggactgc tcttatactg taaggccaga 7320agcacaccag
tcacactaag caaagatcaa ctgagtggta taaataatat tgcatttagt
7380aactaaataa aaatagcacc taatcatgtt cttacaatgg tttactatct
gctcatagac 7440aacccatctg tcattggatt ttcttaaaat ctgaacttca
tcgaaactct catctataaa 7500ccatctcact tacactattt aagtagattc
ctagtttata gttatataaa acacaattgc 7560atgccagatt aacttaccat
ctgtaaaaat gaaaactggg gcaaatatgt cacgaaggaa 7620tccttgcaaa
tttgaaattc gaggtcattg cttaaatggt aagaggtgtc attttagtca
7680taattatttt gaatggccac cccatgcact gcttgtaaga caaaacttta
tgttaaacag 7740aatacttaag tctatggata aaagtataga taccttatca
gaaataagtg gagctgcaga 7800gttggacaga acagaagagt atgctcttgg
tgtagttgga gtgctagaga gttatatagg 7860atcaataaac aatataacta
aacaatcagc atgtgttgcc atgagcaaac tcctcactga 7920actcaatagt
gatgatatca aaaagctgag ggacaatgaa gagctaaatt cacccaagat
7980aagagtgtac aatactgtca tatcatatat tgaaagcaac aggaaaaaca
ataaacaaac 8040tatccatctg ttaaaaagat tgccagcaga cgtattgaag
aaaaccatca aaaacacatt 8100ggatatccat aagagcataa ccatcaacaa
cccaaaagaa tcaactgtta gtgatacaaa 8160tgaccatgcc aaaaataatg
atactacctg acaaatatcc ttgtagtata acttccatac 8220taataacaag
tagatgtaga gttactatgt ataatcaaaa gaacacacta tatttcaatc
8280aaaacaaccc aaataaccat atgtactcac cgaatcaaac attcaatgaa
atccattgga 8340cctctcaaga attgattgac acaattcaaa attttctaca
acatctaggt attattgagg 8400atatatatac aatatatata ttagtgtcat
aacactcaat tctaacactc accacatcgt 8460tacattatta attcaaacaa
ttcaagttgt gggacaaaat ggatcccatt attaatggaa 8520attctgctaa
tgtttatcta accgatagtt atttaaaagg tgttatctct ttctcagagt
8580gtaatgcttt aggaagttac atattcaatg gtccttatct caaaaatgat
tataccaact 8640taattagtag acaaaatcca ttaatagaac acatgaatct
aaagaaacta aatataacac 8700agtccttaat atctaagtat cataaaggtg
aaataaaatt agaagaacct acttattttc 8760agtcattact tatgacatac
aagagtatga cctcgtcaga acagattgct accactaatt 8820tacttaaaaa
gataataaga agagctatag aaataagtga tgtcaaagtc tatgctatat
8880tgaataaact agggcttaaa gaaaaggaca agattaaatc caacaatgga
caagatgaag 8940acaactcagt tattacgacc ataatcaaag atgatatact
ttcagctgtt aaagataatc 9000aatctcatct taaagcagac aaaaatcact
ctacaaaaca aaaagacaca atcaaaacaa 9060cactcttgaa gaaattgatg
tgttcaatgc aacatcctcc atcatggtta atacattggt 9120ttaacttata
cacaaaatta aacaacatat taacacagta tcgatcaaat gaggtaaaaa
9180accatgggtt tacattgata gataatcaaa ctcttagtgg atttcaattt
attttgaacc 9240aatatggttg tatagtttat cataaggaac tcaaaagaat
tactgtgaca acctataatc 9300aattcttgac atggaaagat attagcctta
gtagattaaa tgtttgttta attacatgga 9360ttagtaactg cttgaacaca
ttaaataaaa gcttaggctt aagatgcgga ttcaataatg 9420ttatcttgac
acaactattc ctttatggag attgtatact aaagctattt cacaatgagg
9480ggttctacat aataaaagag gtagagggat ttattatgtc tctaatttta
aatataacag 9540aagaagatca attcagaaaa cgattttata atagtatgct
caacaacatc acagatgctg 9600ctaataaagc tcagaaaaat ctgctatcaa
gagtatgtca tacattatta gataagacag 9660tgtccgataa tataataaat
ggcagatgga taattctatt aagtaagttc cttaaattaa 9720ttaagcttgc
aggtgacaat aaccttaaca atctgagtga actatatttt ttgttcagaa
9780tatttggaca cccaatggta gatgaaagac aagccatgga tgctgttaaa
attaattgca 9840atgagaccaa attttacttg ttaagcagtc tgagtatgtt
aagaggtgcc tttatatata 9900gaattataaa agggtttgta aataattaca
acagatggcc tactttaaga aatgctattg 9960ttttaccctt aagatggtta
acttactata aactaaacac ttatccttct ttgttggaac 10020ttacagaaag
agatttgatt gtgttatcag gactacgttt ctatcgtgag tttcggttgc
10080ctaaaaaagt ggatcttgaa atgattataa atgataaagc tatatcacct
cctaaaaatt 10140tgatatggac tagtttccct agaaattaca tgccatcaca
catacaaaac tatatagaac 10200atgaaaaatt aaaattttcc gagagtgata
aatcaagaag agtattagag tattatttaa 10260gagataacaa attcaatgaa
tgtgatttat acaactgtgt agttaatcaa agttatctca 10320acaaccctaa
tcatgtggta tcattgacag gcaaagaaag agaactcagt gtaggtagaa
10380tgtttgcaat gcaaccggga atgttcagac aggttcaaat attggcagag
aaaatgatag 10440ctgaaaacat tttacaattc tttcctgaaa gtcttacaag
atatggtgat ctagaactac 10500aaaaaatatt agaactgaaa gcaggaataa
gtaacaaatc aaatcgctac aatgataatt 10560acaacaatta cattagtaag
tgctctatca tcacagatct cagcaaattc aatcaagcat 10620ttcgatatga
aacgtcatgt atttgtagtg atgtgctgga tgaactgcat ggtgtacaat
10680ctctattttc ctggttacat ttaactattc ctcatgtcac aataatatgc
acatataggc 10740atgcaccccc ctatatagga gatcatattg tagatcttaa
caatgtagat gaacaaagtg 10800gattatatag atatcacatg ggtggcatcg
aagggtggtg tcaaaaacta tggaccatag 10860aagctatatc actattggat
ctaatatctc tcaaagggaa attctcaatt actgctttaa 10920ttaatggtga
caatcaatca atagatataa gcaaaccaat cagactcatg gaaggtcaaa
10980ctcatgctca agcagattat ttgctagcat taaatagcct taaattactg
tataaagagt 11040atgcaggcat aggccacaaa ttaaaaggaa ctgagactta
tatatcacga gatatgcaat 11100ttatgagtaa aacaattcaa cataacggtg
tatattaccc agctagtata aagaaagtcc 11160taagagtggg accgtggata
aacactatac ttgatgattt caaagtgagt ctagaatcta 11220taggtagttt
gacacaagaa ttagaatata gaggtgaaag tctattatgc agtttaatat
11280ttagaaatgt atggttatat aatcagattg ctctacaatt aaaaaatcat
gcattatgta 11340acaataaact atatttggac atattaaagg ttctgaaaca
cttaaaaacc ttttttaatc 11400ttgataatat tgatacagca ttaacattgt
atatgaattt acccatgtta tttggtggtg 11460gtgatcccaa cttgttatat
cgaagtttct atagaagaac tcctgacttc ctcacagagg 11520ctatagttca
ctctgtgttc atacttagtt attatacaaa ccatgactta aaagataaac
11580ttcaagatct gtcagatgat agattgaata agttcttaac atgcataatc
acgtttgaca 11640aaaaccctaa tgctgaattc gtaacattga tgagagatcc
tcaagcttta gggtctgaga 11700gacaagctaa aattactagc gaaatcaata
gactggcagt tacagaggtt ttgagtacag 11760ctccaaacaa aatattctcc
aaaagtgcac aacattatac tactacagag atagatctaa 11820atgatattat
gcaaaatata gaacctacat atcctcatgg gctaagagtt gtttatgaaa
11880gtttaccctt ttataaagca gagaaaatag taaatcttat atcaggtaca
aaatctataa 11940ctaacatact ggaaaaaact tctgccatag acttaacaga
tattgataga gccactgaga 12000tgatgaggaa aaacataact ttgcttataa
ggatacttcc attggattgt aacagagata 12060aaagagagat attgagtatg
gaaaacctaa gtattactga attaagcaaa tatgttaggg 12120aaagatcttg
gtctttatcc aatatagttg gtgttacatc acccagtatc atgtatacaa
12180tggacatcaa atatactaca agcactatat ctagtggcat aattatagag
aaatataatg 12240ttaacagttt aacacgtggt gagagaggac ccactaaacc
atgggttggt tcatctacac 12300aagagaaaaa aacaatgcca gtttataata
gacaagtctt aaccaaaaaa cagagagatc 12360aaatagatct attagcaaaa
ttggattggg tgtatgcatc tatagataac aaggatgaat 12420tcatggaaga
actcagcata ggaacccttg ggttaacata tgaaaaggcc aagaaattat
12480ttccacaata tttaagtgtc aattatttgc atcgccttac agtcagtagt
agaccatgtg 12540aattccctgc atcaatacca gcttatagaa caacaaatta
tcactttgac actagcccta 12600ttaatcgcat attaacagaa aagtatggtg
atgaagatat tgacatagta ttccaaaact 12660gtataagctt tggccttagt
ttaatgtcag tagtagaaca atttactaat gtatgtccta 12720acagaattat
tctcatacct aagcttaatg agatacattt gatgaaacct cccatattca
12780caggtgatgt tgatattcac aagttaaaac aagtgataca aaaacagcat
atgtttttac 12840cagacaaaat aagtttgact caatatgtgg aattattctt
aagtaataaa acactcaaat 12900ctggatctca tgttaattct aatttaatat
tggcacataa aatatctgac tattttcata 12960atacttacat tttaagtact
aatttagctg gacattggat tctgattata caacttatga 13020aagattctaa
aggtattttt gaaaaagatt ggggagaggg atatataact gatcatatgt
13080ttattaattt gaaagttttc ttcaatgctt ataagaccta tctcttgtgt
tttcataaag 13140gttatggcaa agcaaagctg gagtgtgata tgaacacttc
agatcttcta tgtgtattgg 13200aattaataga cagtagttat tggaagtcta
tgtctaaggt atttttagaa caaaaagtta 13260tcaaatacat tcttagccaa
gatgcaagtt tacatagagt aaaaggatgt catagcttca 13320aattatggtt
tcttaaacgt cttaatgtag cagaattcac agtttgccct tgggttgtta
13380acatagatta tcatccaaca catatgaaag caatattaac ttatatagat
cttgttagaa 13440tgggattgat aaatatagat agaatacaca ttaaaaataa
acacaaattc aatgatgaat 13500tttatacttc taatctcttc tacattaatt
ataacttctc agataatact catctattaa 13560ctaaacatat aaggattgct
aattctgaat tagaaaataa ttacaacaaa ttatatcatc 13620ctacaccaga
aaccctagag aatatactag ccaatccgat taaaagtaat gacaaaaaga
13680cactgaatga ctattgtata ggtaaaaatg ttgactcaat aatgttacca
ttgttatcta 13740ataagaagct tattaaatcg tctgcaatga ttagaaccaa
ttacagcaaa caagatttgt 13800ataatttatt ccctatggtt gtgattgata
gaattataga tcattcaggc aatacagcca 13860aatccaacca actttacact
actacttccc accaaatatc cttagtgcac aatagcacat 13920cactttactg
catgcttcct tggcatcata ttaatagatt caattttgta tttagttcta
13980caggttgtaa aattagtata gagtatattt taaaagatct taaaattaaa
gatcccaatt 14040gtatagcatt cataggtgaa ggagcaggga atttattatt
gcgtacagta gtggaacttc 14100atcctgacat aagatatatt tacagaagtc
tgaaagattg caatgatcat agtttaccta 14160ttgagttttt aaggctgtac
aatggacata tcaacattga ttatggtgaa aatttgacca 14220ttcctgctac
agatgcaacc aacaacattc attggtctta tttacatata aagtttgctg
14280aacctatcag tctttttgtc tgtgatgccg aattgtctgt aacagtcaac
tggagtaaaa 14340ttataataga atggagcaag catgtaagaa agtgcaagta
ctgttcctca gttaataaat 14400gtatgttaat agtaaaatat catgctcaag
atgatattga tttcaaatta gacaatataa 14460ctatattaaa aacttatgta
tgcttaggca gtaagttaaa gggatcggag gtttacttag 14520tccttacaat
aggtcctgcg aatatattcc cagtatttaa tgtagtacaa aatgctaaat
14580tgatactatc aagaaccaaa aatttcatca tgcctaagaa agctgataaa
gagtctattg 14640atgcaaatat taaaagtttg ataccctttc tttgttaccc
tataacaaaa aaaggaatta 14700atactgcatt gtcaaaacta aagagtgttg
ttagtggaga tatactatca tattctatag 14760ctggacgtaa tgaagttttc
agcaataaac ttataaatca taagcatatg aacatcttaa 14820aatggttcaa
tcatgtttta aatttcagat caacagaact aaactataac catttatata
14880tggtagaatc tacatatcct tacctaagtg aattgttaaa cagcttgaca
accaatgaac 14940ttaaaaaact gattaaaatc acaggtagtc tgttatacaa
ctttcataat gaataatgaa 15000taaagatctt ataataaaaa ttcccatagc
tatacactaa cactgtattc aattatagtt 15060attaaaaatt aaaaatcata
taatttttta aataactttt agtgaactaa tcctaaagtt 15120atcattttaa
tcttggagga ataaatttaa accctaatct aattggttta tatgtgtatt
15180aactaaatta cgagatatta gtttttgaca ctttttttct cgt
15223215225DNARespiratory Syncytial Virus 2acgcgaaaaa atgcgtacta
caaacttgca cattcggaaa aaatggggca aataagaatt 60tgataagtgc tatttaagtc
taaccttttc aatcagaaat ggggtgcaat tcactgagca 120tgataaaggt
tagattacaa aatttatttg acaatgacga agtagcattg ttaaaaataa
180catgttatac tgacaaatta attcttctga ccaatgcatt agccaaagca
gcaatacata 240caattaaatt aaacggtata gtttttatac atgttataac
aagcagtgaa gtgtgccctg 300ataacaacat tgtagtaaaa tctaacttta
caacaatgcc aatattacaa aacggaggat 360acatatggga attgattgag
ttgacacact gctctcaatt aaacggtcta atggatgata 420attgtgaaat
caaattttct aaaagactaa gtgactcagt aatgactaat tatatgaatc
480aaatatctga tttacttggg cttgatctca attcatgaat tatgtttagt
ctaactcaat 540agacatgtgt ttattaccat tttagttaat ataaaaactc
atcaaaggga aatggggcaa 600ataaactcac ctaatcaatc aaactatgag
cactacaaat gacaacacta ctatgcaaag 660attaatgatc acggacatga
gacccctgtc gatggattca ataataacat ctctcaccaa 720agaaatcatc
acacacaaat tcatatactt gataaacaat gaatgtattg taagaaaact
780tgatgaaaga caagctacat ttacattctt agtcaattat gagatgaagc
tactgcacaa 840agtagggagt accaaataca agaaatacac tgaatataat
acaaaatatg gcactttccc 900catgcctata tttatcaatc atggcgggtt
tctagaatgt attggcatta agcctacaaa 960acacactcct ataatataca
aatatgacct caacccgtaa attccaacaa aaaaaaccaa 1020cccaaccaaa
ccaagctatt cctcaaacaa caatgctcaa tagttaagaa ggagctaatc
1080cgttttagta attaaaaata aaagtaaagc caataacata aattggggca
aatacaaaga 1140tggctcttag caaagtcaag ttaaatgata cattaaataa
ggatcagctg ctgtcatcca 1200gcaaatacac tattcaacgt agtacaggag
ataatattga cactcccaat tatgatgtgc 1260aaaaacacct aaacaaacta
tgtggtatgc tattaatcac tgaagatgca aatcataaat 1320tcacaggatt
aataggtatg ttatatgcta tgtccaggtt aggaagggaa gacactataa
1380agatacttaa agatgctgga tatcatgtta aagctaatgg agtagatata
acaacatatc 1440gtcaagatat aaatggaaag gaaatgaaat tcgaagtatt
aacattatca agcttgacat 1500cagaaataca agtcaatatt gagatagaat
ctagaaaatc ctacaaaaaa atgctaaaag 1560agatgggaga agtggctcca
gaatataggc atgattctcc agactgtggg atgataatac 1620tgtgtatagc
agcacttgta ataaccaaat tagcagcagg agacagatca ggtcttacag
1680cagtaattag gagggcaaac aatgtcttaa aaaatgaaat aaaacgctac
aagggtctca 1740taccaaagga tatagctaac agtttttatg aagtgtttga
aaaacaccct catcttatag 1800atgtttttgt gcactttggc attgcacaat
catcaacaag agggggtagt agagttgaag 1860gaatctttgc aggattgttt
atgaatgcct atggttcagg gcaagtaatg ctaagatggg 1920gagttttagc
caaatctgta aaaaatatca tgctaggtca tgctagtgtc caggcagaaa
1980tggagcaagt tgtggaagtc tatgagtatg cacagaagtt gggaggagaa
gctggattct 2040accatatatt gaacaatcca aaagcatcat tgctgtcatt
aactcaattt cctaacttct 2100caagtgtggt cctaggcaat gcagcaggtc
taggcataat gggagagtat agaggtacgc 2160caagaaacca ggatctttat
gatgcagcca aagcatatgc agagcaactc aaagaaaatg 2220gagtaataaa
ctacagtgta ttagacttaa cagcagaaga attggaagcc ataaagaatc
2280aactcaaccc taaagaagat gatgtagagc tttaagttaa caaaaaatac
ggggcaaata 2340agtcaacatg gagaagtttg cacctgaatt tcatggagaa
gatgcaaata acaaagctac 2400caaattccta gaatcaataa agggcaagtt
cgcatcatcc aaagatccta agaagaaaga 2460tagcataata tctgttaact
caatagatat agaagtaacc aaagagagcc cgataacatc 2520tggcaccaac
atcatcaatc caacaagtga agccgacagt accccagaaa ccaaagccaa
2580ctacccaaga aaacccctag taagcttcaa agaagatctc accccaagtg
acaacccttt 2640ttctaagttg tacaaagaaa caatagaaac atttgataac
aatgaagaag aatctagcta 2700ctcatatgaa gagataaatg atcaaacaaa
tgacaacatt acagcaagac tagatagaat 2760tgatgaaaaa ttaagtgaaa
tattaggaat gctccataca ttagtagttg caagtgcagg 2820acccacttca
gctcgcgatg gaataagaga tgctatggtt ggtctgagag aagaaatgat
2880agaaaaaata agagcggaag cattaatgac caatgatagg ttagaggcta
tggcaagact 2940taggaatgag gaaagcgaaa aaatggcaaa agacacctca
gatgaagtgc ctcttaatcc 3000aacttccaaa aaattgagtg acttgttgga
agacaacgat agtgacaatg atctgtcact 3060tgatgatttt tgatcagtga
tcaactcact cagcaatcaa caacatcaat aaaacagaca 3120tcaatccatt
gaatcaactg ccagaccgaa caaacaaatg tccgtcagcg gaaccaccaa
3180ccaatcaatc aaccaactga tccatcagca acctgacgaa attaacaata
tagtaacaaa 3240aaaagaacaa gatggggcaa atatggaaac atacgtgaac
aagcttcacg aaggctccac 3300atacacagca gctgttcagt acaatgttct
agaaaaagat gatgatcctg catcactaac 3360aatatgggtg cctatgttcc
agtcatctgt accagcagac ttgctcataa aagaacttgc 3420aagcatcaac
atactagtga agcagatctc tacgcccaaa ggaccttcac tacgagtcac
3480gattaactca agaagtgctg tgctggctca aatgcctagt aatttcatca
taagcgcaaa 3540tgtatcatta gatgaaagaa gcaaattagc atatgatgta
actacacctt gtgaaatcaa 3600agcatgcagt ctaacatgct taaaagtgaa
aagtatgtta actacagtca aagatcttac 3660catgaagaca ttcaacccca
ctcatgagat cattgctcta tgtgaatttg aaaatattat 3720gacatcaaaa
agagtaataa taccaaccta tctaagacca attagtgtca aaaacaagga
3780tctgaactca ctagaaaaca tagcaaccac cgaattcaaa aatgctatca
ccaatgcgaa 3840aattattccc tatgctggat tagtattagt tatcacagtt
actgacaata aaggagcatt 3900caaatatatc aagccacaga gtcaatttat
agtagatctt ggtgcctacc tagaaaaaga 3960gagcatatat tatgtgacta
ctaattggaa gcatacagct acacgttttt caatcaaacc 4020actagaggat
taaatttaat tatcaacact gaatgacagg tccacatata tcctcaaact
4080acacactata tccaaacatc atgaacatct acactacaca cttcatcaca
caaaccaatc 4140ccactcaaaa tccaaaatca ctaccagcca ctatctgcta
gacctagagt gcgaataggt 4200aaataaaacc aaaatatggg gtaaatagac
attagttaga gttcaatcaa tctcaacaac 4260catttatacc gccaattcaa
tacatatact ataaatctta aaatgggaaa tacatccatc 4320acaatagaat
tcacaagcaa attttggccc tattttacac taatacatat gatcttaact
4380ctaatctctt tactaattat aatcactatt atgattgcaa tactaaataa
gctaagtgaa 4440cataaaacat tctgtaacaa tactcttgaa ctaggacaga
tgcatcaaat caacacatag 4500tgctctacca tcatgctgtg tcaaattata
atcctgtata tataaacaaa caaatccaat 4560cttctcacag agtcatggtg
tcgcaaaacc acgccaacta tcatggtagc atagagtagt 4620tatttaaaaa
ttaacataat gatgaattat tagtatggga tcaaaaacaa cattggggca
4680aatgcaacca tgtccaaaca caagaatcaa cgcactgcca ggactctaga
aaagacctgg 4740gatactctca atcatctaat tgtaatatcc tcttgtttat
acagattaaa tttaaaatct 4800atagcacaaa tagcactatc agttctggca
atgataatct caacctctct cataattgca 4860gccataatat tcatcatctc
tgccaatcac aaagttacac taacaacggt cacagttcaa 4920acaataaaaa
accacactga aaaaaacatc accacctacc ttactcaagt cccaccagaa
4980agggttagct catccaaaca acctacaacc acatcaccaa tccacacaaa
ttcagccaca 5040acatcaccca acacaaagtc agaaacacac cacacaacag
cacaaaccaa aggcagaacc 5100accacctcaa cacagaccaa caagccgagc
acaaaaccac gcctaaaaaa tccaccaaaa 5160aaaccaaaag atgattacca
ttttgaagtg ttcaacttcg ttccctgtag tatatgtggc 5220aacaatcaac
tttgcaaatc catctgtaaa acaataccaa gcaacaaacc aaagaagaaa
5280ccaaccatca aacccacaaa caaaccaacc accaaaacca caaacaaaag
agacccaaaa 5340acaccagcca aaacgacgaa aaaagaaact accaccaacc
caacaaaaaa accaaccctc 5400acgaccacag aaagagacac cagcacctca
caatccactg tgctcgacac aaccacatta 5460gaacacacaa tccaacagca
atccctccac tcaaccaccc ccgaaaacac acccaactcc 5520acacaaacac
ccacagcatc cgagccctct acatcaaatt ccacccaaaa tacccaatca
5580catgcttagt tattcaaaaa ctacatctta gcagaaaacc gtgacctatc
aagcaagaac 5640gaaattaaac ctggggcaaa taaccatgga gctgctgatc
cacaggttaa gtgcaatctt 5700cctaactctt gctattaatg cattgtacct
cacctcaagt cagaacataa ctgaggagtt 5760ttaccaatcg acatgtagtg
cagttagcag aggttatttt agtgctttaa gaacaggttg 5820gtataccagt
gtcataacaa tagaattaag taatataaaa gaaaccaaat gcaatggaac
5880tgacactaaa gtaaaactta taaaacaaga attagataag tataagaatg
cagtgacaga 5940attacagcta cttatgcaaa acacaccagc tgccaacaac
cgggccagaa gagaagcacc 6000acagtatatg aactatacaa tcaataccac
taaaaaccta aatgtatcaa taagcaagaa 6060gaggaaacga agatttctgg
gcttcttgtt aggtgtagga tctgcaatag caagtggtat 6120agctgtatcc
aaagttctac accttgaagg agaagtgaac aagatcaaaa atgctttgtt
6180atctacaaac aaagctgtag tcagtctatc aaatggggtc agtgttttaa
ccagcaaagt 6240gttagatctc aagaattaca taaataacca attattaccc
atagtaaatc aacagagctg 6300tcgcatctcc aacattgaaa cagttataga
attccagcag aagaacagca gattgttgga 6360aatcaacaga gaattcagtg
tcaatgcagg tgtaacaaca cctttaagca cttacatgtt 6420aacaaacagt
gagttactat cattgatcaa tgatatgcct ataacaaatg atcagaaaaa
6480attaatgtca agcaatgttc agatagtaag gcaacaaagt tattctatca
tgtctataat 6540aaaggaagaa gtccttgcat atgttgtaca gctacctatc
tatggtgtaa tagatacacc 6600ttgctggaaa ttacacacat cacctctatg
caccaccaac atcaaagaag gatcaaatat 6660ttgtttaaca aggactgata
gaggatggta ttgtgataat gcaggatcag tatccttctt 6720tccacaggct
gacacttgta aagtacagtc caatcgagta ttttgtgaca ctatgaacag
6780tttgacatta ccaagtgaag tcagcctttg taacactgac atattcaatt
ccaagtatga 6840ctgcaaaatt atgacatcaa aaacagacat aagcagctca
gtaattactt ctcttggagc 6900tatagtgtca tgctatggta aaactaaatg
cactgcatcc aacaaaaatc gtgggattat 6960aaagacattt tctaatggtt
gtgactatgt gtcaaacaaa ggagtagata ctgtgtcagt 7020gggcaacact
ttatactatg taaacaagct ggaaggcaag aacctttatg taaaagggga
7080acctataata aattactatg accctctagt gtttccttct gatgagtttg
atgcatcaat 7140atctcaagtc aatgaaaaaa tcaatcaaag tttagctttt
attcgtagat ctgatgaatt 7200actacataat gtaaatactg gcaaatctac
tacaaatatt atgataacta caattattat 7260agtaatcatt gtagtattgt
tatcattaat agctattggt ttgctgttgt attgcaaagc 7320caaaaacaca
ccagttacac taagcaaaga ccaactaagt ggaatcaata atattgcatt
7380cagcaaatag acaaaaaacc acctgatcat gtttcaacaa cagtctgctg
atcaccaatc 7440ccaaatcaac ccataacaaa cacttcaaca tcacagtaca
ggctgaatca tttcttcaca 7500tcatgctacc cacacaacta agctagatcc
ttaactcata gttacataaa aacctcaagt 7560atcacaatca aacactaaat
caacacatca ttcacaaaat taacagctgg ggcaaatatg 7620tcgcgaagaa
atccttgtaa atttgagatt agaggtcatt gcttgaatgg tagaagatgt
7680cactacagtc ataattactt tgaatggcct cctcatgcct tactagtgag
gcaaaacttc 7740atgttaaaca agatactcaa gtcaatggac aaaagcatag
acactttgtc tgaaataagt 7800ggagctgctg aactggacag aacagaagaa
tatgctcttg gtatagttgg agtgctagag 7860agttacatag gatctataaa
caacataaca aaacaatcag catgtgttgc tatgagtaaa 7920cttcttattg
agatcaatag tgatgacatt aaaaagctga gagataatga agaacccaat
7980tcacctaaga taagagtgta caatactgtt atatcataca ttgagagcaa
tagaaaaaac 8040aacaagcaaa caatccatct gctcaaaaga ctaccagcag
acgtgctgaa gaagacaata 8100aaaaacacat tagatatcca caaaagcata
atcataagca acccaaaaga gtcaaccgtg 8160aatgatcaaa atgaccaaac
caaaaataat gatattaccg gataaatatc cttgtagtat 8220atcatccata
ttgatttcaa gtgaaagcat gattgctaca ttcaatcata aaaacatatt
8280acaatttaac cataaccatt tggataacca ccagcgttta ttaaataata
tatttgatga 8340aattcattgg acacctaaaa acttattaga tgccactcaa
caatttctcc aacatcttaa 8400catccctgaa gatatatata caatatatat
attagtgtca taatgcttgg ccataacgat 8460tctatatcat ccaaccataa
aactatctta ataaggttat gggacaaaat ggatcccatt 8520attaatggaa
actctgctaa tgtgtatcta actgatagtt atttaaaagg tgttatctct
8580ttttcagaat gtaatgcttt agggagttac ctttttaacg gcccttatct
caaaaatgat 8640tacaccaact taattagtag acaaagtcca ctactagagc
atatgaatct taaaaaacta 8700actataacac agtcattaat atctagatat
cataaaggtg aactgaaatt agaagaacca 8760acttatttcc agtcattact
tatgacatat aaaagcatgt cctcgtctga acaaattgct 8820acaactaact
tacttaaaaa aataatacga agagctatag aaataagtga tgtaaaggtg
8880tacgccatct tgaataaact aggactaaag gaaaaggaca gagttaagcc
caacaataat 8940tcaggtgatg aaaactcagt acttacaact ataattaaag
atgatatact ttcggctgtg 9000gaaagcaatc aatcatatac aaattcagac
aaaaatcact cagtaaatca aaatatcact 9060atcaaaacaa cactcttgaa
aaaattgatg tgttcaatgc aacatcctcc atcatggtta 9120atacactggt
tcaatttata tacaaaatta aataacatat taacacaata tcgatcaaat
9180gaggtaaaaa gtcatgggtt tatattaata gataatcaaa ctttaagtgg
ttttcagttt 9240attttaaatc aatatggttg tatcgtttat cataaaggac
tcaaaaaaat cacaactact 9300acttacaatc aatttttaac atggaaagac
atcagcctta gcagattaaa tgtttgctta 9360attacttgga taagtaattg
tttgaataca ttaaataaaa gcttagggct gagatgtgga 9420ttcaataatg
ttgtgttatc acaattattt ctttatggag attgtatact gaaattattt
9480cataatgaag gcttctacat aataaaagaa gtagagggat ttattatgtc
tttaattcta 9540aacataacag aagaagatca atttaggaaa cgattttata
atagcatgct aaataacatc 9600acagatgcag ctattaaggc tcaaaagaac
ctactatcaa gggtatgtca cactttatta 9660gacaagacag tgtctgataa
tatcataaat ggtaaatgga taatcctatt aagtaaattt 9720cttaaattga
ttaagcttgc aggtgataat aatctcaata atttgagtga gctatatttt
9780ctcttcagaa tctttggaca tccaatggtt gatgaaagac aagcaatgga
tgctgtaaga 9840attaactgta atgaaactaa gttctactta ttaagtagtc
taagtacgtt aagaggtgct 9900ttcatttata gaatcataaa agggtttgta
aatacctaca acagatggcc cactttaagg 9960aatgctattg tcctacctct
aagatggtta aactattata aacttaatac ttatccatct 10020ctacttgaaa
tcacagaaaa tgatttgatt attttatcag gattgcggtt ctatcgtgaa
10080tttcatctgc ctaaaaaagt ggatcttgaa atgataataa atgacaaagc
catttcacct 10140ccaaaagatc taatatggac tagttttcct agaaattaca
tgccatcaca tatacaaaat 10200tatatagaac atgaaaagtt gaagttctct
gaaagcgaca gatcaagaag agtactagag 10260tattacttga gagataataa
attcaatgaa tgcgatctat acaattgtgt agtcaatcaa 10320agctatctca
acaactctaa tcacgtggta tcactaactg gtaaagaaag agagctcagt
10380gtaggtagaa tgtttgctat gcaaccaggt atgtttaggc aaatccaaat
cttagcagag 10440aaaatgatag ccgaaaatat tttacaattc ttccctgaga
gtttgacaag atatggtgat 10500ctagagcttc aaaagatatt agaattaaaa
gcaggaataa gcaacaagtc aaatcgttat 10560aatgataact acaacaatta
tatcagtaaa tgttctatca ttacagatct tagcaaattc 10620aatcaagcat
ttagatatga aacatcatgt atctgcagtg atgtattaga tgaactgcat
10680ggagtacaat ctctgttctc ttggttgcat ttaacaatac ctcttgtcac
aataatatgt 10740acatatagac atgcacctcc tttcataaag gatcatgttg
ttaatcttaa tgaagttgat 10800gaacaaagtg gattatacag atatcatatg
ggtggtattg agggctggtg tcaaaaactg 10860tggaccattg aagctatatc
attattagat ctaatatctc tcaaagggaa attctctatc 10920acagctctga
taaatggtga taatcagtca attgatataa gtaaaccagt tagacttata
10980gagggtcaga cccatgctca agcagattat ttgttagcat taaatagcct
taaattgcta 11040tataaagagt atgcaggtat aggccataag cttaagggaa
cagagaccta tatatcccga 11100gatatgcagt tcatgagcaa aacaatccag
cacaatggag tgtactatcc agccagtatc 11160aaaaaagtcc tgagagtagg
tccatggata aatacaatac ttgatgattt taaagttagt 11220ttagaatcta
taggtagctt aacacaggag ttagaataca gaggggaaag cttattatgc
11280agtttaatat ttaggaacat ttggttatac aatcaaattg ctttgcaact
ccgaaatcat 11340gcattatgta acaataagct atatttagat atattgaaag
tattaaaaca cttaaaaact 11400ttttttaatc ttgatagtat cgatatggcg
ttatcattgt atatgaattt gcctatgctg 11460tttggtggtg gtgatcctaa
tttgttatat cgaagctttt ataggagaac tccagacttc 11520cttacagaag
ctatagtaca ttcagtgttt gtgttgagct attatactgg tcacgattta
11580caagataagc tccaggatct tccagatgat agactgaaca aattcttgac
atgtgtcatc 11640acattcgata aaaatcccaa tgccgagttt gtaacattga
tgagggatcc acaggcgtta 11700gggtctgaaa ggcaagctaa aattactagt
gagattaata gattagcagt aacagaagtc 11760ttaagtatag ctccaaacaa
aatattttct aaaagtgcac aacattatac taccactgag 11820attgatctaa
atgacattat gcaaaatata gaaccaactt accctcatgg attaagagtt
11880gtttatgaaa gtctaccttt ttataaagca gaaaaaatag ttaatcttat
atcaggaaca 11940aaatccataa ctaatatact tgaaaaaaca tcagcaatag
atacaactga tattaatagg 12000gctactgata tgatgaggaa aaatataact
ttacttataa ggatacttcc actagattgt 12060aacaaagaca aaagagagtt
attaagttta gaaaatctta gtataactga attaagcaag 12120tatgtaagag
aaagatcttg gtcattatcc aatatagtag gagtaacatc gccaagtatt
12180atgttcacaa tggacattaa atatacaact agcactatag ccagtggtat
aattatagaa 12240aaatataatg ttaatagttt aactcgtggt gaaagaggac
ctactaagcc atgggtaggt 12300tcatctacgc aggagaaaaa aacaatgcca
gtgtacaata gacaagtttt aaccaaaaag 12360caaagagacc aaatagattt
attagcaaaa ttagactggg tatatgcatc catagacaac 12420aaagatgaat
tcatggaaga actgagtact ggaacacttg gactgtcata tgaaaaagcc
12480aaaaagttgt ttccacaata tctaagtgtc aattatttac accgtttaac
agtcagtagt 12540agaccatgtg aattccctgc atcaatacca gcttatagaa
caacaaatta tcatttcgat 12600actagtccta tcaatcatgt attaacagaa
aagtatggag atgaagatat cgacattgtg 12660tttcaaaatt gcataagttt
tggtcttagc ctgatgtcgg ttgtggaaca attcacaaac 12720atatgtccta
atagaattat tctcataccg aagctgaatg agatacattt gatgaaacct
12780cctatattta caggagatgt tgatatcatc aagttgaagc aagtgataca
aaaacagcat 12840atgttcctac cagataaaat aagtttaacc caatatgtag
aattattcct aagtaacaaa 12900gcacttaaat ctggatctaa catcaattct
aatttaatat tagtacataa aatgtctgat 12960tattttcata atgcttatat
tttaagtact aatttagctg gacattggat tctaattatt 13020caacttatga
aagattcaaa aggtattttt gaaaaagatt ggggagaggg gtacataact
13080gatcatatgt tcattaattt gaatgttttc tttaatgctt ataagactta
tttgctatgt 13140tttcataaag gttatggtaa agcaaaatta gaatgtgata
tgaacacttc agatcttctt 13200tgtgttttgg agttaataga cagtagctac
tggaaatcta tgtctaaagt tttcctagaa 13260caaaaagtca taaaatacat
agtcaatcaa gacacaagtt tgcatagaat aaaaggctgt 13320cacagtttta
agttgtggtt tttaaaacgc cttaataatg ctaaatttac cgtatgccct
13380tgggttgtta acatagatta tcacccaaca catatgaaag ctatattatc
ttacatagat 13440ttagttagaa tggggttaat aaatgtagat aaattaacca
ttaaaaataa aaacaaattc 13500aatgatgaat tttacacatc aaatctcttt
tacattagtt ataacttttc agacaacact 13560catttgctaa caaaacaaat
aagaattgct aattcagaat tagaagataa ttataacaaa 13620ctatatcacc
caaccccaga aactttagaa aatatatcat taattcctgt taaaagtaat
13680aatagtaaca aacctaaatt ttgtataagt ggaaataccg aatctataat
gatgtcaaca 13740ttctctaata aaatgcatat taaatcttcc actgttacca
caagattcaa ttatagcaaa 13800caagacttgt acaatttatt tccaaatgtt
gtgatagaca ggattataga tcattcaggt 13860aatacagcaa aatctaacca
actttacatc accacttcac atcagacatc tttagtaagg 13920aatagtgcat
cactttattg catgcttcct tggcatcatg tcaatagatt taactttgta
13980tttagttcca caggatgcaa gatcagtata gagtatattt taaaagatct
taagattaag 14040gaccccagtt gtatagcatt cataggtgaa ggagctggta
acttattatt acgtacggta 14100gtagaacttc atccagacat aagatacatt
tacagaagtt taaaagattg caatgatcat 14160agtttaccta ttgaatttct
aagattatac aacgggcata taaacataga ttatggtgag 14220aatttaacca
ttcctgctac agatgcaact aataacattc attggtctta tttacatata
14280aaatttgcag aacctattag catctttgtc tgcgatgctg aattacctgt
tacagccaat 14340tggagtaaaa ttataattga atggagtaag catgtaagaa
agtgcaagta ctgttcttct 14400gtaaatagat gcattttaat cgcaaaatat
catgctcaag atgatattga tttcaaatta 14460gataacatta ctatattaaa
aacttacgtg tgcctaggta gcaagttaaa aggatctgaa 14520gtttacttag
tccttacaat aggccctgca aatatacttc ctgtttttga tgttgtgcaa
14580aatgctaaat tgattttttc aagaactaaa aatttcatta tgcctaaaaa
aactgacaag 14640gaatctatcg atgcaaatat taaaagctta atacctttcc
tttgttaccc tataacaaaa 14700aaaggaatta agacttcatt gtcaaaattg
aagagtgtag ttaatgggga tatattatca 14760tattctatag ctggacgtaa
tgaagtattc agcaacaagc ttataaacca caagcatatg
14820aatatcctaa aatggctaga tcatgtttta aattttagat cagctgaact
taattacaat 14880catttataca tgatagagtc cacatatcct tacttaagtg
aattgttaaa tagtttaaca 14940accaatgagc tcaagaaact gattaaaata
acaggtagtg tactatacaa ccttcccaac 15000gaacagtaac ttaaaatatc
attaacaagt ttggtcaaat ttagatgcta acacatcatt 15060atattatagt
tattaaaaaa tatgcaaact tttcaataat ttagcttact gattccaaaa
15120ttatcatttt atttttaagg ggttgaataa aagtctaaaa ctaacaatga
tacatgtgca 15180tttacaacac aacgagacat tagtttttga cacttttttt ctcgt
15225333DNAArtificial SequencePositive-sense M gene fragment
3actcaaataa gttaataaaa aatatcccgg gat 33431DNAArtificial
SequenceNegative-sense M gene fragment 4cccgggatat tttttattaa
cttatttgag t 31518DNAArtificial SequencePositive-sense primer
uptream of SH gene 5gaaagtatat attatgtt 18620DNAArtificial
SequenceNegative-sense primer downstream of SH gene 6tatataagca
cgatgatatg 20716DNAArtificial SequencePositive-sense M gene
fragment 7actcaaataa gttaat 16814DNAArtificial
SequenceNegative-sense M gene fragment 8taacttattt gagt
14928DNAArtificial SequenceForward PCR primer for NS1 gene deletion
9gacacaaccc acaatgataa tacaccac 281032DNAArtificial SequenceReverse
PCR primer for NS1 gene deletion 10catctctaac caagggagtt aaatttaagt
gg 321127DNAArtificial SequenceForward PCR primer for NS2 gene
deletion 11ttaaggagag atataagata gaagatg 271227DNAArtificial
SequenceReverse PCR primer for NS2 gene deletion 12gttttatatt
aactaatggt gttagtg 271333DNAArtificial SequenceForward PCR primer
for ablation of G gene start site 13ttataattgc agccatcata
ttcatagcct cgg 331430DNAArtificial SequenceReverse PCR primer for
ablation of G gene start site 14gtgaagttga gattacaatt gccagaatgg
301548DNAArtificial SequencePositive-sense primer for intergenic
region preceding the G gene 15gcatggatcc ttaattaaaa attaacataa
tgatgaatta ttagtatg 481651DNAArtificial SequenceNegative-sense
primer for intergenic region downstream of F gene 16gtgttggatc
ctgattgcat gcttgaggtt tttatgtaac tatgagttaa g 511713DNAArtificial
SequenceDescription of Artificial Sequence G gene-end signal
17agttattcaa aaa 131848DNAArtificial SequencePositve-sense primer
with G gene-end and F gene-start signals 18ccacgcctaa tgagttatat
aaaacaattg gggcaaataa ccatggag 481946DNAArtificial
SequenceNegative-sense primer with G gene-end and F gene-start
signals 19gactgagtgt tctgagtaga gttggatgta gagggctcgg atgctg
462012DNAArtificial SequenceDescription of Artificial Sequence F
gene-end signal of RSV A2 20agttatataa aa 122113DNAArtificial
SequenceG gene-end signal of RSV A2 21agttacttaa aaa
132251RNAArtificial SequenceSynthetic oligonucleotide 22aaaanuuaag
gagagauaua agauagaaga uggggcaaau acaamsaugg c 512353RNAArtificial
SequenceSynthetic oligonucleotide 23uuaaaaacau auuaucacaa
aargccwuga ccaacuuaaa cagaaucaaa aua 532451RNAArtificial
SequenceSynthetic oligonucleotide 24aaacacaauu gmaugccaga
uuaacuuacc aucuguaaaa augaaaacug g 512573DNAArtificial
SequenceSynthetic oligonucleotide 25ccaaaaaagt cccgggtcaa
aaatggggca aataagaatt tgataagtac cacttaaatt 60taactctaga atg
732649DNAArtificial SequenceSynthetic oligonucleotide 26taactgcagt
attcaattat agttattaaa aattaacccg ggaaatcat 492727DNAArtificial
SequenceSynthetic oligonucleotide 27atgagaccgt wgtmacytga gaccata
27289PRTArtificial SequenceSynthetic peptide 28Met Arg Pro Leu Ser
Leu Glu Thr Ile1 52913DNAArtificial SequenceSynthetic
oligonucleotide 29agttaatata aaa 133013DNAArtificial
SequenceSynthetic oligonucleotide 30agttaataaa aaa
133112DNAArtificial SequenceSynthetic oligonucleotide 31agtaatttaa
aa 123213DNAArtificial SequenceSynthetic oligonucleotide
32agttaataaa aaa 13339PRTArtificial SequenceSynthetic peptide 33Ile
Leu Ala Xaa Xaa Ile Ser Thr Ser1 53427RNAArtificial
SequenceSynthetic oligonucleotide 34auucuggcaa ukruaaucuc aacuuca
273543DNAArtificial SequenceSynthetic oligonucleotide 35actataaagt
agttaattaa aaattaacat aatgatgaat tat 433654DNAArtificial
SequenceSynthetic oligonucleotide 36cttaactcat agttacataa
aaacctcaag catgccagat taacttacca tctg 543766DNAArtificial
SequenceSynthetic oligonucleotide 37tccaactcta ctcagaacac
tcagtcccac gcctaatgag ttatataaaa caattggggc 60aaataa
663811PRTArtificial SequenceSynthetic peptide 38Ser Asn Ser Thr Gln
Asn Thr Gln Ser His Ala1 5 10
* * * * *