U.S. patent application number 10/909641 was filed with the patent office on 2005-07-14 for quantitative epstein barr virus pcr rapid assay.
Invention is credited to Groen, Pamela A., Witte, David P..
Application Number | 20050153278 10/909641 |
Document ID | / |
Family ID | 23023011 |
Filed Date | 2005-07-14 |
United States Patent
Application |
20050153278 |
Kind Code |
A1 |
Groen, Pamela A. ; et
al. |
July 14, 2005 |
Quantitative epstein barr virus PCR rapid assay
Abstract
The present invention provides novel compositions comprising
Epstein-Barr virus-specific oligonucleotides that are useful as
primers to amplify particular regions of the genome during
enzymatic nucleic acid amplification. The invention also provides a
rapid, sensitive and specific method for the detection and
quantitation of the virus which may be present in a clinical
specimen, using the virus-specific primers and enzymatic nucleic
acid amplification; hybridization of amplified target sequences, if
present, with one or more Epstein-Barr virus-specific
oligonucleotide probes which are labeled with a detectable moiety;
and detection of the detectable moiety of labeled oligonucleotide
probe hybridized to amplified target sequences of Epstein-Barr
virus DNA.
Inventors: |
Groen, Pamela A.;
(Clarksville, OH) ; Witte, David P.; (Cincinnati,
OH) |
Correspondence
Address: |
Stephen R. Albainy-Jenei
Frost Brown Todd LLC
2200 PNC Center, 201 East Fifth Street
Cincinnati
OH
45202
US
|
Family ID: |
23023011 |
Appl. No.: |
10/909641 |
Filed: |
August 2, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10909641 |
Aug 2, 2004 |
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10074620 |
Feb 13, 2002 |
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6790952 |
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60268439 |
Feb 13, 2001 |
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Current U.S.
Class: |
435/5 ;
536/23.72 |
Current CPC
Class: |
C12Q 1/705 20130101 |
Class at
Publication: |
435/005 ;
435/006; 536/023.72 |
International
Class: |
C12Q 001/70; C12Q
001/68; C07H 021/04 |
Claims
What is claimed is:
1. An isolated and purified oligonucleotide primer for enzymatic
amplification of Epstein-Barr virus DNA, consisting essentially of
a nucleic acid sequence which complements and specifically
hybridize to a nucleic acid sequence of an Epstein-Barr virus under
stringent conditions, which encodes a conserved EBNAZ region of the
Epstein Barr virus genome, wherein the nucleic acid sequence is at
least 80% homologous to a sequence selected from the group
consisting of SEQ ID NO:1, SEQ ID NO. 2, SEQ ID NO:5, and SEQ ID
NO:6.
2. An isolated and purified oligonucleotide primer for enzymatic
amplification of Epstein-Barr virus DNA, consisting essentially of
a nucleic acid sequence which complements and specifically
hybridize to a nucleic acid sequence of an Epstein-Barr virus under
stringent conditions, which encodes a conserved EBNAZ region of the
Epstein Barr virus genome, wherein the nucleic acid sequence is at
least 95% homologous to a sequence selected from the group
consisting of SEQ ID NO:5, and SEQ ID NO:6.
3. An isolated and purified oligonucleotide primer pair for
enzymatic amplification of Epstein-Barr virus DNA, consisting
essentially of a pair of nucleic acid sequences which complement
and specifically hybridize to a nucleic acid sequence of an
Epstein-Barr virus under stringent conditions, which encodes a
conserved EBNAZ region of the Epstein Barr virus genome, wherein
the pair of nucleic acid sequences is at least 95% homologous to
sequences SEQ ID NO:5 and SEQ ID NO:6.
4. An isolated and purified oligonucleotide primer pair for
enzymatic amplification of Epstein-Barr virus DNA consisting
essentially of a pair of nucleic acid sequences which complement
and specifically hybridize to a nucleic acid sequence of an
Epstein-Barr virus nucleic acid molecule, under stringent
conditions, which encodes a conserved EBNAZ region of the
Epstein-Barr virus genome, wherein the pair of nucleic acid
sequences is selected from the group consisting of (a) the
oligonucleotide pair of SEQ ID NO:5 and SEQ ID NO:6, and (b) a
nucleotide pair which differs from SEQ ID NO:5 and SEQ ID NO:6 by a
one base change or substitution therein.
5. A method of detecting the presence of Epstein Barr virus DNA in
a sample comprising: a) contacting the sample with a hybridization
probe comprising one or more oligonucleotides selected from the
group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7 and SEQ
ID NO:8, labeled with a detectable moiety, under suitable
conditions permitting hybridization of the labeled oligonucleotide
probe to the Epstein-Barr virus DNA, and b) detecting the presence
of the probe bound to the DNA sequences by detecting the detectable
moiety of the labeled oligonucleotide probe hybridized to the
Epstein Barr virus DNA sequences.
6. A method of detecting the presence of Epstein Barr virus DNA in
a sample comprising: a) contacting the sample with an
oligonucleotide primer selected from the group consisting of SEQ ID
NO:1, SEQ. ID NO. 2, SEQ ID NO:5, SEQ ID NO:6, under suitable
conditions permitting hybridization of the oligonucleotides to the
Epstein Barr virus DNA, b) enzymatically amplifying a region of the
Epstein Barr virus DNA using the oligonucleotide primer sequence
selected from the group consisting of SEQ ID NO:1, SEQ. ID NO. 2,
SEQ ID NO:5, SEQ ID NO:6, to form amplified Epstein Barr virus DNA
sequences, c) contacting the amplified Epstein Barr virus DNA
sequences from step (b), if present, with a hybridization probe
comprising one or more oligonucleotides selected from the group
consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:7 and SEQ ID
NO:8, labeled with a detectable moiety under suitable conditions
permitting hybridization of the labeled oligonucleotide probe to
the amplified Epstein Barr virus DNA sequences, and d) detecting
the presence of the amplified Epstein Barr virus DNA sequences by
detecting the detectable moiety of the labeled oligonucleotide
probe hybridized to the amplified Epstein Barr virus DNA
sequences.
7. A method of detecting the presence of Epstein Barr virus DNA in
a sample comprising: a) contacting the sample with oligonucleotide
primer pair of SEQ ID NO:1 and SEQ. ID NO. 2 or the oligonucleotide
pair of SEQ ID NO:5 and SEQ ID NO:6, under suitable conditions
permitting hybridization of the oligonucleotides to the Epstein
Barr virus DNA, b) enzymatically amplifying a region of the Epstein
Barr virus DNA using the oligonucleotide pair of SEQ ID NO:1 and
SEQ. ID NO. 2 or the oligonucleotide pair of SEQ ID NO:5 and SEQ ID
NO:6 to form amplified Epstein Barr virus DNA sequences, c)
contacting the amplified Epstein Barr virus DNA sequences from step
(b), if present, with a hybridization probe comprising one or more
oligonucleotides selected from the group consisting of SEQ ID NO:3,
SEQ ID NO:4, SEQ ID NO:7 and SEQ ID NO:8, labeled with a detectable
moiety under suitable conditions permitting hybridization of the
labeled oligonucleotide probe to the amplified Epstein Barr virus
DNA sequences, and d) detecting the presence of the amplified
Epstein Barr virus DNA sequences by detecting the detectable moiety
of the labeled oligonucleotide probe hybridized to the amplified
Epstein Barr virus DNA sequences.
8. A method of detecting the presence of Epstein Barr virus DNA in
a sample comprising: a) contacting the sample with oligonucleotide
primer pair of SEQ ID NO:5 and SEQ ID NO:6 under suitable
conditions permitting hybridization of the oligonucleotides to the
Epstein Barr virus DNA, b) enzymatically amplifying a region of the
Epstein Barr virus DNA using the oligonucleotide pair of SEQ ID
NO:5 and SEQ ID NO:6 to form nucleic acid amplification products,
c) contacting the amplified Epstein Barr virus DNA sequences from
step (b), if present, with hybridization probes comprising the
oligonucleotide pair of SEQ ID NO:3 and SEQ ID NO:4 or the
oligonucleotide pair of SEQ ID NO:7 and SEQ ID NO:8, labeled with a
detectable moiety under suitable conditions permitting
hybridization of the labeled oligonucleotide probe to amplified
Epstein Barr virus DNA sequences, and d) detecting the presence of
amplified Epstein Barr virus DNA sequences by detecting the
detectable moiety of the labeled oligonucleotide probe hybridized
to the amplified Epstein Barr virus DNA sequence.
9. The method of claim 9, wherein the sample is treated to release
nucleic acid molecules from cells in the sample prior to step
(a).
10. The method of claim 9, wherein the presence of the amplified
Epstein Barr virus DNA sequences hybridized to labeled
oligonucleotide probe correlates to the presence of Epstein Barr
virus in the sample.
11. The method of claim 11, wherein the amplified DNA sequence is
from the EBNAZ region of the Epstein Barr virus genome.
12. The method of claim 11, additionally comprising adding an
internal standard for accessing relative amounts of Epstein Barr
virus after amplification.
13. The method of claim 11, wherein presence of the amplified
Epstein Ban-virus DNA sequences hybridized to labeled
oligonucleotide probe is correlated to the presence of Epstein Barr
virus in the sample by comparing the amount of amplification
product to the quantity of amplification products formed from known
Internal standards.
14. The method of claim 11, wherein the primers comprise the
oligonucleotide pair of SEQ ID NO:1 and SEQ ID NO:2.
15. The method of claim 15, wherein the hybridization probes
comprise SEQ ID NO:3 and SEQ ID NO:4.
16. The method of claim 11, wherein the primers comprise the
oligonucleotide pair of SEQ ID NO:5 and SEQ ID NO:6.
17. The method of claim 17, wherein the hybridization probes
comprise SEQ ID NO:7 and SEQ ID NO:8.
18. The method of claim 11, wherein the amplification is performed
by cyclic polymerase-mediated reaction.
19. The method of claim 19, wherein the cyclic polymerase-mediated
reaction is an enzymatic assay selected from the group consisting
of PCR, LCR, SDA, QBRA, 3SR, and NASBA.
20. The method of claim 20, wherein the polymerase is selected from
the group consisting of thermostable polymerase, E. coli DNA pol 1,
Klenow fragment, and 1-7DNA polymerase.
21. The method of claim 21, wherein the PCR is a thermocyclic
reaction.
22. The method of claim 11, wherein the detectable moiety is
selected from the group consisting of a digoxigenin-dUTP, biotin,
calorimetric, fluorescent, chemiluminescent,
electrochemiluminescent signal and a radioactive component.
23. The method of claim 11, wherein the detectable moiety is a
fluorescent component generating a fluorescent signal.
24. The method of claim 21, wherein the amount of amplification
product is determined simultaneously with respect to the PCR
amplification step.
25. A method of selecting an appropriate dosage or type of
antiviral agent for treating an infection caused by Epstein Barr
virus comprising the steps of: a) obtaining a sample from a patient
to be treated; b) preparing the sample for PCR amplification; c)
adding PCR reagents to the prepared sample, including at least one
primer pair selected from the group consisting of the
oligonucleotide pair SEQ ID NO:5 and SEQ ID NO:6, and complementary
sequences thereof; d) maintaining the prepared sample of step c
under conditions suitable for amplification; e) adding at least one
probe labeled with a detectable moiety corresponding to the primer
pair, selected from the group consisting of the oligonucleotide
pair of SEQ ID NO:3 and SEQ ID NO:4, the oligonucleotide pair of
SEQ ID NO:7 and SEQ ID NO:8, and complementary sequences thereof,
under suitable conditions permitting hybridization; f) measuring
quantitatively one or more of the Epstein Barr virus species
contained in the sample; and g) selecting the type or adjusting the
dosage of the antiviral agent based on the quantitative
measurement.
26. The method of claim 26 additionally comprising adding to step
c) an internal standard for accessing relative amounts of Epstein
Barr virus after amplification.
27. The method of claim 27, wherein the PCR reagents comprise a
polymerase selected from the group consisting of thermostable
polymerase, E. coli DNA pol I, Klenow fragment, and T7 DNA
polymerase.
28. The method of claim 28, wherein the detectable moiety is
selected from the group consisting of a digoxigenin-dUTP, biotin,
calorimetric, fluorescent, chemiluminescent,
electrochemiluminescent signal and a radioactive component.
29. The method of claim 20, further comprising a separation step
wherein the amplified product is isolated.
30. A method for the simultaneous amplification and detection of
Epstein Barr Virus DNA in a sample comprising: a) processing the
sample to produce denatured opposing strands of DNA; b)
simultaneously subjecting the denatured opposing strands of DNA to
polymerase chain reaction in the presence of: i) an aqueous
solution buffered to a pH of about 6 to about 9; and ii) first and
second primers which are specific to and hybridizable with the
denatured opposing strands of DNA, wherein the sequences of the
first and second primers are SEQ ID NO:5 and SEQ ID NO:6, and c)
simultaneously detecting the amplified DNA using hybridization
probes comprising the oligonucleotide pair of SEQ ID NO:3 and SEQ
ID NO:4 or the oligonucleotide pair of SEQ ID NO:7 and SEQ ID
NO:8.
31. The method of claim 31 wherein the hybridization probe further
comprises a detectable moiety selected from the group consisting of
a chemiluminescent component, a fluorescent component, and a
radioactive component.
32. A diagnostic test kit for detection of Epstein Barr virus
comprising: (a) one oligonucleotide primer pair of SEQ ID NO:5 and
SEQ ID NO:6 and (b) at least one oligonucleotide probe labeled with
a detectable moiety selected from the group consisting SEQ ID NO:3,
SEQ ID NO:4, SEQ ID NO:7 and SEQ ID NO:8.
33. The diagnostic test kit of claim 33, further comprising at
least one additional reagent selected from the group consisting of
a lysing buffer for lysing cells contained in the specimen; enzyme
amplification reaction components dNTPS, reaction buffer, and
amplifying enzyme; and a combination thereof.
34. The diagnostic kit of claim 34, wherein the primers comprise
the oligonucleotide pair of SEQ ID NO: 1 and SEQ ID NO:2.
35. The diagnostic kit of claim 35, wherein the hybridization
probes comprise SEQ ID NO:3 and SEQ ID NO:4.
36. The diagnostic kit of claim 34, wherein the primers comprise
the oligonucleotide pair of SEQ ID NO:5 and SEQ ID NO:6.
37. The diagnostic kit of claim 37, wherein the hybridization
probes comprise SEQ ID NO:7 and SEQ ID NO:8.
38. The diagnostic kit of claim 33, wherein the hybridization probe
further comprises a detectable moiety selected from the group
consisting of a chemiluminescent component, a fluorescent
component, and a radioactive component.
39. The oligonucleotide primer pair of claim 3, wherein the pair of
oligonucleotides consists of sequences of from 10 to 35 nucleotides
each, and wherein the oligonucleotides are the same as or
complementary to at least nine contiguous nucleic acids from the
oligonucleotide pairs of SEQ ID NO:1 and SEQ ID NO:2 and (b) the
oligonucleotide pair of SEQ ID NO:5 and SEQ ID NO:6.
40. The oligonucleotide primer pair of claim 3, wherein the pair of
oligonucleotides consists of sequences of from 18 to 26 nucleotides
each, and wherein the oligonucleotides are the same as or
complementary to at least nine contiguous nucleic acids from the
oligonucleotide pairs of SEQ ID NO: 1 and SEQ ID NO:2 and (b) the
oligonucleotide pair of SEQ ID NO:5 and SEQ ID NO:6.
Description
[0001] This application is a divisional of patent application Ser.
No. 10/074,620, filed Feb. 13, 2002, which claims the benefit under
35 USC 119(e) of U.S. Provisional Patent Application Ser. No.
60/268,439, filed Feb. 13, 2001, which applications are hereby
incorporated by reference in their entirety.
BACKGROUND OF THE INVENTION
[0002] The invention relates generally to novel compositions and
methods for detecting the presence of viruses that frequently
infect humans and are associated with the development of human
disease. More particularly, the invention is directed to an
accurate and sensitive method for the diagnosis and quantitation of
Epstein-Barr virus infection using specific oligonucleotides as
primers to amplify particular regions of the genome of the virus
sought to be detected in a clinical specimen. Epstein-Barr
virus-specific oligonucleotides may be used in the subsequent
detection of the amplified regions of DNA.
[0003] Epstein-Barr virus (EBV), a human herpes virus, is
ubiquitous in humans. Antibodies to polypeptides of the virus are
present in over 80% of human serum samples from the United States
and in even higher percentages from populations in Asia and Africa.
Although it is prevalent throughout the world, the consequences of
EBV infection vary among different populations. The virus is
responsible for of infectious mononucleosis, a benign proliferation
of infected B-lymphocytes, in Western countries and is implicated
in Burkitt's lymphoma in Africa and nasopharyngeal carcinoma (NPC)
in Asia. EBV can also cause acute and rapidly progressive B
lymphoproliferative disease in severely immune compromised
patients.
[0004] As a result of the immunosuppression necessary to maintain
the function of transplanted organs, transplant patients are all at
risk for developing EBV infection and therefore post transplant
lymphoproliferative disorder (PTLD). However, the group at highest
risk for this complication is the liver transplant population. This
is because these patients are generally very young, frequently less
than 5 years of age, and therefore they frequently have not yet
been exposed to EBV and as a result do not have a natural immunity
to the virus.
[0005] Approximately 50% of the transplanted population develop EBV
infection during the post-transplant course, frequently symptomatic
including PTLD. These patients therefore are a prime population for
monitoring the development of EBV infection and its associated
complications. Approximately 50% of these patients will develop EBV
infection requiring monitoring of the peripheral blood EBV DNA
levels.
[0006] Nationally there are between 450-500 liver transplants in
pediatric patients. In those patients under 14 months of age
approximately 75% of them develop EBV infections. These numbers do
not include all the bone marrow, kidney, heart, and lung
transplants in pediatric patients. And although there is a lower
incidence of EBV lymphoproliferative complication in all of the
adult transplant patients, there is a clinically significant
incidence of this complication in these patients as well. The
demand for this kind of patient monitoring therefore is high.
Currently, there are a few recognized labs who provide quantitative
EBV analyses.
[0007] EBV associated post-transplant lymphoproliferative disease
(PTLD) is a major cause of morbidity and mortality for children and
adults who undergo solid organ transplantation and bone marrow
transplantation (Ho M, et al. The frequency of Epstein-Barr virus
infection and associated lymphoproliferative syndrome after
transplantation and its manifestations in children. Transplantation
45: 719-727, 1988).
[0008] Patients who are EBV nave and receive an organ from an EBV
positive donor, especially those treated with anti-T-cell
immunotherapy (anti-thymocyte globulin or monoclonal antibodies),
are at high risk for developing PTLD. Infants and toddlers, who
comprise 50% of the pediatric liver transplant population, are
usually EBV nave. More than 75% of patients at risk acquire the
virus within the first year of life. Up to 15% of liver transplant
recipients who are at high risk will develop PTLD. Consequently,
the risk of infection and complication is substantial.
[0009] For children, especially those less than two years of age,
PTLD is a critical factor affecting cost, graft function and
quality of life. Attempts to treat these transplant patients with
interferon, acyclovir, and anti-B cell monoclonal antibodies are
generally not successful once an EBV infection has been established
or reactivated (Papadopoulos E B, et al. Infusions of donor
leukocytes as treatment of Epstein-Barr virus associated
lymphoproliferative disorder complicating allogeneic marrow
transplantation. N Engl J Med 330: 1185, 1994; Zutter M M, et al.
Epstein-Barr virus lymphoproliferation after bone marrow
transplantation. Blood 72, 520, 1988; Shapiro R S, et al.
Epstein-Barr virus associated B-cell lymphoproliferative disorders
following bone marrow transplantation. Blood 71: 1234, 1988; Antin
J et al. Selective depletion of bone marrow T lymphocytes with
anti-CD5 monoclonal antibodies: Effective prophylaxis for
graft-vs-host disease in patients with hematologic malignancies.
Blood: 78: 2139, 1991; Martin P J, et al. Fatal Epstein-Barr virus
associated proliferation of donor B cells after treatment of acute
graft vs-host disease with a murine anti-T-cell antibody. Ann
Intern Med 101: 310, 1984). A number of studies however have shown
that PTLD may be reversible in solid-organ transplant recipients
following reduction or discontinuation of immune suppression
(Starzl T, et al. Reversibility of lymphomas and
lymphoproliferative lesions developing under cyclosporin steroid
therapy. Lancet I: 583, 1984).
[0010] Differences in levels of EBV DNA found in the peripheral
blood post-transplant may distinguish which patients are at highest
risk to develop EBV PTLD and therefore could permit earlier
intervention in these patients. Previous studies have shown a
correlation between levels of EBV DNA and the occurrence of
EBV-PLTD in organ transplant patients (Kenagy D N, et al.
Epstein-Barr virus DNA in peripheral blood leukocytes with
post-transplant lymphoproliferative disease. Transplant 60: 547,
1995; Riddler S A, et al. Increased levels of circulating
Epstein-Barr virus (EBV) infected lymphocytes and decreased EBV
nuclear antigen antibody responses are associated with the
development of post-transplant lymphoproliferative disease in
solid-organ transplant recipients Blood 84: 972, 1994; Savoie A, et
al. Direct correlation between the load of Epstein-Barr virus
infected lymphocytes in the peripheral blood of pediatric
transplant patients and risk of lymphoproliferative disease. Blood
83: 2715, 1994). These results suggest the potential benefit of
monitoring EBV DNA levels in the peripheral blood of the transplant
patients may be clinically useful in the management and possible
preemptive intervention of the development of PTLD in these
patients. As a result, a number of assays using a variety of
approaches have been developed and reported for either
semiquantitative or quantitative determination of EBV DNA
levels.
[0011] Most of the semiquantitative assays are based on standard
PCR analysis of a dilution series of patient samples compared to a
known standard. While extremely useful, quantitative PCR can be
very laborious to perform. Most of the difficulties arise because
only a very small number of the cycles in a PCR reaction contain
useful information. The early cycles have undetectable amounts of
the DNA product and late cycles (plateau phase) are almost as
uninformative. The PCR product is then detected by gel
electrophoresis followed by ethidium bromide staining of the gel.
The result is determined by the lowest dilution at which a band is
visible (Lucas K G, et al. Semiquantitative Epstein-Barr virus
polymerase chain reaction for the determination of patients at risk
for EBV induced lymphoproliferative disease after stem cell
transplantation. Blood 91: 3654, 1998; Baldanti F, et al. High
levels of Epstein-Barr virus DNA in blood of solid organ transplant
recipients and their value in predicting post-transplant
lymphoproliferative disorders. J. Clin Microbiol. 38: 613, 2000;
Rogers B, et al. Epstein-Barr virus polymerase chain reaction and
serology in pediatric post-transplant lymphoproliferative disorder:
three year experience. Pediatric & Developmental Pathology 1:
480, 1998). The quantification of the PCR and RT-PCR products is
therefore based on an endpoint approach rather than using a kinetic
approach. Since some labs use probe specific confirmation of their
PCR products and others do not, the specificity and sensitivity of
these assays are quite variable.
[0012] The standards used for the quantitative determinations also
vary, and even the sample preparation differs as some assays base
the results on the number of copies per ml of whole blood, others
use the number of isolated white blood cells as the basis, while
still other labs base the determination on extracted total DNA
quantity.
[0013] More recently the introduction of "real-time" quantitative
PCR analysis has been developed for the determination of EBV viral
DNA levels (Niesters H et al. Development of a real-time
quantitative assay for detection of Epstein-Barr virus. J Clin
Microbiol. 2000 February; 38(2): 712-5). Real-time or kinetic PCR
is a powerful method for determining the initial template copy
number. The quantitative information in a PCR reaction comes from
the few cycles where the amount of DNA grows logarithmically from
barely above background to the plateau. Often only 6 to 8 cycles
out of 40 will fall in this log-linear portion of the curve. Since
the fluorescence signal is acquired during each cycle, data from
the critical cycles can be captured, quantified and the
fluorescence plotted against the cycle number.
[0014] This technology has improved the dynamic range in which
samples can be analyzed quantitatively without dilution which
reduces substantially the turnaround time and is much less labor
intensive and less prone to technical errors due to less
manipulation involved (Kimura H, et al. Quantitative analysis of
Epstein-Barr virus load by using a real-time PCR assay. J. Clin
Microbiol. 37: 132, 1999; Martell M, et al. High-throughput
real-time reverse transcription-PCR quantitation of hepatitis C
virus RNA J Clin Microbiol. 1999 February; 37(2): 327-32; Mercier
B, et al. Simultaneous screening for HBV DNA and HCV RNA genomes in
blood donations using a novel TaqMan PCR assay. J Virol Methods.
1999 January; 77(1): 1-9). This latter approach provides the best
opportunity to provide routine monitoring of the transplant patient
population for early evidence of EBV infection. Early detection and
recognition of patients at high risk for PTLD will provide
opportunities for preemptive therapy rather than treating and
managing the complications of advanced PTLD.
[0015] Therefore, it would be advantageous to have an accurate and
sensitive method for the diagnosis and quantitation of Epstein-Barr
virus infection in a clinical specimen.
STATEMENT OF THE INVENTION
[0016] It is an object of the present invention to disclose a
nucleic acid sequences (oligonucleotides) useful as primers and/or
probes in the detection of a Epstein-Barr virus in clinical
specimens. Also, the present invention is directed to a method of
detecting the presence of Epstein-Barr virus in a clinical specimen
wherein the oligonucleotides of the present invention may be used
to amplify target nucleic acid sequences of a Epstein-Barr virus
that may be contained within a clinical specimen, and/or to detect
the presence or absence of amplified target nucleic acid sequences
of the Epstein-Barr virus. Respective oligonucleotides may be used
to amplify and/or detect EBV and EBV nucleic acid sequences. By
using the oligonucleotides of the present invention and according
to the methods of the present invention, as few as one to ten
copies of the Epstein-Barr virus genome may be detected.
[0017] One object of the present invention is to provide
oligonucleotides that can be used as primers to amplify specific
nucleic acid sequences of EBV.
[0018] Another object of the present invention is to provide
oligonucleotides that can be used as probes in the detection of
amplified specific nucleic acid sequences of EBV.
[0019] Among the nucleic acids provided herein are the nucleic
acids whose sequence is provided in SEQ ID NO:1, SEQ ID NO:2, SEQ
ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:70R SEQ
ID NO:8, or a fragment thereof. Additionally, the invention
includes mutant or variant nucleic acids of SEQ ID NO:1, SEQ ID
NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8, or a fragment thereof, any of whose bases may
be changed from the corresponding bases shown in SEQ ID NO:1, SEQ
ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8, while still hybridizing to an EBV DNA
sequence. The invention further includes the complement of the
nucleic acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ
ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8,
including fragments, derivatives, analogs and homologs thereof. The
invention additionally includes nucleic acids or nucleic acid
fragments, or complements thereto, whose structures include
chemical modifications.
[0020] The invention also includes an oligonucleotide that includes
a portion of the disclosed nucleic acids. For example, the
oligonucleotide can be at least 10 nucleotides in length and
include at least nine contiguous nucleotides of SEQ ID NO:1, SEQ ID
NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8.
[0021] A further object of the present invention is to provide an
accurate and sensitive method for detecting the presence of EBV
that may be contained in clinical specimens by using the
oligonucleotides disclosed to amplify and detect specific nucleic
acid sequences of EBV.
[0022] Another object of the present invention is to provide
oligonucleotides that can be used as primers to amplify specific
nucleic acid sequences of EBV.
[0023] Another object of the present invention is to provide
oligonucleotides that can be used as probes in the detection of
amplified specific nucleic acid sequences of EBV.
[0024] Another object of the present invention is to provide
oligonucleotides that can be used as primers to amplify DNA
sequences from the EBNA2 region of the EBV genome.
[0025] A further object of the present invention is to provide an
accurate and sensitive method for detecting the presence of EBV
that may be contained in clinical specimens by using the
oligonucleotides disclosed to amplify and detect specific nucleic
acid sequences of EBV.
[0026] It is a further object of the invention to provide a kit for
identifying or amplifying a gene encoding an Epstein-Barr virus
polypeptide.
[0027] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, suitable methods and materials are described below. All
publications, patent applications, patents, and other references
mentioned herein are incorporated by reference in their entirety.
In the case of conflict, the present specification, including
definitions, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting.
[0028] Other features and advantages of the invention will be
apparent from the following detailed description and claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0029] FIG. 1 is a diagrammatic representation of the Epstein-Barr
Virus genomic map (GenBank Accession #K0333).
DETAILED DESCRIPTION OF THE INVENTION
[0030] In the description that follows, a number of terms used in
recombinant DNA technology are extensively utilized. In order to
provide a clear and consistent understanding of the specification
and claims, including the scope to be given such terms, the
following definitions are provided.
[0031] An "amplification primer" is an oligonucleotide that is
capable of annealing adjacent to a target sequence and serving as
an initiation point for DNA synthesis when placed under conditions
in which synthesis of a primer extension product which is
complementary to a nucleic acid strand is initiated.
[0032] A "coding sequence" or "open reading frame" is a nucleotide
sequence that is transcribed and translated into a polypeptide in
vivo when placed under the control of appropriate regulatory
sequences. The boundaries of the coding sequence are determined by
a start codon at the 5' (amino) terminus and a translation stop
codon at the 3' (carboxyl) terminus. A coding sequence can include,
but is not limited to, prokaryotic sequences, cDNA from eukaryotic
mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA,
and even synthetic DNA or RNA sequences. A polyadenylation signal
and transcription termination sequence will usually be located 3'
to the coding sequence.
[0033] By the term "complementarity" or "complementary" is meant,
for the purposes of the specification or claims, a sufficient
number in the oligonucleotide of complementary base pairs in its
sequence to interact specifically (hybridize) with the target
nucleic acid sequence of the Epstein-Barr virus to be amplified or
detected. As known to those skilled in the art, a very high degree
of complementarity is needed for specificity and sensitivity
involving hybridization, although it need not be 100%. Thus, for
example, an oligonucleotide that is identical in nucleotide
sequence to an oligonucleotide disclosed herein, except for one
base change or substitution, may function equivalently to the
disclosed oligonucleotides. A "complementary DNA" or "cDNA" gene
includes recombinant genes synthesized by reverse transcription of
messenger RNA ("mRNA").
[0034] By the term "composition" is meant, for the purposes of the
specification or claims, a combination of elements which may
include one or more of the following: the reaction buffer for the
respective method of enzymatic amplification, plus one or more
oligonucleotides specific for Epstein-Barr virus, wherein said
oligonucleotide is labeled with a detectable moiety.
[0035] By the terms "consisting essentially of a nucleotide
sequence" is meant, for the purposes of the specification or
claims, the nucleotide sequence disclosed, and also encompasses
nucleotide sequences which are identical except for a one base
change or substitution therein.
[0036] A "cyclic polymerase-mediated reaction" refers to a
biochemical reaction in which a template molecule or a population
of template molecules is periodically and repeatedly copied to
create a complementary template molecule or complementary template
molecules, thereby increasing the number of the template molecules
over time. Generally, a "cyclic polymerase-mediated reaction"
includes primer molecules that serve to initiate synthesis of the
complementary template, a polymerase enzyme that catalyzes the
synthesis, and monomeric molecules that make up the template. In
each cycle of a "cyclic polymerase-mediated reaction" not every
template will necessarily by copied, and each complementary
template whose synthesis is initiated in a cycle will not
necessarily be completed. In preferred embodiments of this
invention, the template and primer molecules are nucleic acids, the
monomeric units are nucleotides, and the polymerase is a DNA or RNA
polymerase.
[0037] "Denaturation" of a template molecule refers to the
unfolding or other alteration of the structure of a template so as
to make the template accessible to duplication. In the case of DNA,
"denaturation" refers to the separation of the two complementary
strands of the double helix, thereby creating two complementary,
single stranded template molecules. "Denaturation" can be
accomplished in any of a variety of ways, including by heat or by
treatment of the DNA with a base or other denaturant.
[0038] A "detectable amount of product" refers to an amount of
amplified nucleic acid that can be detected using standard
laboratory tools. Generally, a "detectable amount of product" is
between about 10 ng and about 100 ng of DNA. A "detectable marker"
refers to a nucleotide analog that allows detection using visual or
other means. For example, fluorescently labeled nucleotides can be
incorporated into a nucleic acid during one or more steps of a
cyclic polymerase-mediated reaction, thereby allowing the detection
of the product of the reaction using, e.g. fluorescence microscopy
or other fluorescence-detection instrumentation.
[0039] By the term "detectable moiety" is meant, for the purposes
of the specification or claims, a label molecule (isotopic or
non-isotopic) which is incorporated indirectly or directly into an
oligonucleotide, wherein the label molecule facilitates the
detection of the oligonucleotide in which it is incorporated when
the oligonucleotide is hybridized to amplified Epstein-Barr virus
sequences. Thus, "detectable moiety" is used synonymously with
"label molecule". Synthesis of oligonucleotides can be accomplished
by any one of several methods known to those skilled in the art. To
label an oligonucleotide with a detectable moiety, detectable
moiety-labeled dUTP may be added in the process of synthesizing the
oligonucleotide so that the detectable moiety is incorporated
directly into the oligonucleotide. Alternatively, the detectable
moiety may be incorporated "indirectly" such as, for example, by
biotinylating the 5' aminogroup of the oligonucleotide with
sulfo-NHS-biotin. Other label molecules, known to those skilled in
the art as being useful for detection, include chemiluminescent or
fluorescent molecules. Various fluorescent molecules are known in
the art which are suitable for use to label a nucleic acid
substrate for the method of the present invention. Fluorescent
molecules used as labels may include amine-reactive molecules which
are reactive to end terminal amines of the substrate; sulfonyl
chlorides which are conjugated to the substrate through amine
residues; and the like. Depending on the fluorescent molecule used,
incorporating the substrate with the fluorescent molecule label
include attachment by covalent or noncovalent means. The protocol
for such incorporation may vary depending upon the fluorescent
molecule used. Such protocols are known in the art for the
respective fluorescent molecule.
[0040] "DNA amplification" as used herein refers to any process
that increases the number of copies of a specific DNA sequence by
enzymatically amplifying the nucleic acid sequence. A variety of
processes are known. One of the most commonly used is the
Polymerase Chain Reaction (PCR) process of Mullis as described in
U.S. Pat. Nos. 4,683,195 and 4,683,202. PCR involves the use of a
thermostable DNA polymerase, known sequences as primers, and
heating cycles, which separate the replicating deoxyribonucleic
acid (DNA), strands and exponentially amplify a gene of interest.
Any type of PCR, such as quantitative PCR, RTPCR, hot start PCR,
LAPCR, multiplex PCR, touchdown PCR, etc., may be used. Preferably,
quantitative PCR is used. In general, the PCR amplification process
involves an enzymatic chain reaction for preparing exponential
quantities of a specific nucleic acid sequence. It requires a small
amount of a sequence to initiate the chain reaction and
oligonucleotide primers that will hybridize to the sequence. In PCR
the primers are annealed to denatured nucleic acid followed by
extension with an inducing agent (enzyme) and nucleotides. This
results in newly synthesized extension products. Since these newly
synthesized sequences become templates for the primers, repeated
cycles of denaturing, primer annealing, and extension results in
exponential accumulation of the specific sequence being amplified.
The extension product of the chain reaction will be a discrete
nucleic acid duplex with a termini corresponding to the ends of the
specific primers employed.
[0041] "DNA" refers to the polymeric form of deoxyribonucleotides
(adenine, guanine, thymine, or cytosine) in its either single
stranded form, or a double-stranded helix. This term refers only to
the primary and secondary structure of the molecule, and does not
limit it to any particular tertiary forms. Thus, this term includes
double-stranded DNA found, inter alia, in linear DNA molecules
(e.g., restriction fragments), viruses, plasmids, and chromosomes.
In discussing the structure of particular double-stranded DNA
molecules, sequences may be described herein according to the
normal convention of giving only the sequence in the 5' to 3'
direction along the nontranscribed strand of DNA (i.e., the strand
having a sequence homologous to the mRNA).
[0042] By the terms "enzymatically amplify" or "amplify" is meant,
for the purposes of the specification or claims, DNA amplification,
i.e., a process by which nucleic acid sequences are amplified in
number. There are several means for enzymatically amplifying
nucleic acid sequences. Currently the most commonly used method is
the polymerase chain reaction (PCR).
[0043] Other amplification methods include LCR (ligase chain
reaction) which utilizes DNA ligase, and a probe consisting of two
halves of a DNA segment that is complementary to the sequence of
the DNA to be amplified, enzyme QB replicase and a ribonucleic acid
(RNA) sequence template attached to a probe complementary to the
DNA to be copied which is used to make a DNA template for
exponential production of complementary RNA; strand displacement
amplification (SDA); Q.beta. replicase amplification (Q.beta.RA);
self-sustained replication (3SR); and NASBA (nucleic acid
sequence-based amplification), which can be performed on RNA or DNA
as the nucleic acid sequence to be amplified.
[0044] The "extension of the primer molecules" refers to the
addition of nucleotides to a primer molecule so as to synthesize a
nucleic acid complementary to a template molecule. "Extension of
the primer molecules" does not necessarily imply that the primer
molecule is extended to synthesize a complete complementary
template molecule. Rather, even if only a fraction of the template
molecule has been copied, the primer is still considered
extended.
[0045] A "fragment" of a molecule such as a protein or nucleic acid
is meant to refer to any portion of the amino acid or nucleotide
genetic sequence.
[0046] As used herein, "fluorescence resonance energy transfer
pair" or "FRET pair" refers to a pair of fluorophores comprising a
donor fluorophore and acceptor fluorophore, wherein the donor
fluorophore is capable of transferring resonance energy to the
acceptor fluorophore. In other words the emission spectrum of the
donor fluorophore overlaps the absorption spectrum of the acceptor
fluorophore. In preferred fluorescence resonance energy transfer
pairs, the absorption spectrum of the donor fluorophore does not
substantially overlap the absorption spectrum of the acceptor
fluorophore. As used herein, "a donor oligonucleotide probe" refers
to an oligonucleotide that is labeled with a donor fluorophore of a
fluorescent resonance energy transfer pair. As used herein, "an
acceptor oligonucleotide probe" refers to an oligonucleotide that
is labeled with an acceptor fluorophore of a fluorescent resonance
energy transfer pair. As used herein, "FRET oligonucleotide pair"
refers to the donor oligonucleotide probe and the acceptor
oligonucleotide probe pair that form a fluorescence resonance
energy transfer relationship when the donor oligonucleotide probe
and the acceptor oligonucleotide probe are both hybridized to their
complementary target nucleic acid sequences. Two separate FRET
oligonucleotide pairs, each specific for one locus and each
comprising a different acceptor dye may be used at the same time.
Acceptable fluorophore pairs for use as fluorescent resonance
energy transfer pairs are well know to those skilled in the art and
include, but are not limited to, fluorescein/rhodamine,
phycoerythrin/Cy7, fluorescein/Cy5, fluorescein/Cy5.5,
fluorescein/LC Red 640, and fluorescein/LC Red 705.
[0047] A "functional derivative" of a sequence, either protein or
nucleic acid, is a molecule that possesses a biological activity
(either functional or structural) that is substantially similar to
a biological activity of the protein or nucleic acid sequence. A
functional derivative of a protein may or may not contain
post-translational modifications such as covalently linked
carbohydrate, depending on the necessity of such modifications for
the performance of a specific function. The term "functional
derivative" is intended to include the "fragments," "segments,"
"variants," "analogs," or "chemical derivatives" of a molecule.
[0048] A "heterologous" region of a DNA or RNA construct is an
identifiable segment of DNA or RNA molecule within a larger nucleic
acid that is not found in association with the larger molecule in
nature. For instance, when the heterologous region encodes a
mammalian gene, the gene will usually be flanked by DNA that does
not flank the mammalian genomic DNA in the genome of the source
organism. Another example of a heterologous coding sequence is a
construct where the coding sequence itself is not found in nature
(e.g., a cDNA where the genomic coding sequence contains introns,
or synthetic sequences having codons different than the native
gene). Allelic variations or naturally-occurring mutational events
do not give rise to a heterologous region of DNA as defined
herein.
[0049] The term "hybridization" refers to the principle that two
single-stranded nucleic acid molecules that have complementary base
sequences will reform the thermodynamically favored double-stranded
structure if they are mixed under the proper conditions. The
double-stranded structure will be formed between two complementary
single-stranded nucleic acids even if one is immobilized. The term
"standard hybridization conditions" in general refers to salt and
temperature conditions substantially equivalent to 5.times.SSC and
65.degree. C. for both hybridization and wash. However, one skilled
in the art will appreciate that such "standard hybridization
conditions" are dependent on particular conditions including the
concentration of sodium and magnesium in the buffer, nucleotide
sequence length and concentration, percent mismatch, percent
formamide, and the like. Also important in the determination of
"standard hybridization conditions" is whether the two sequences
hybridizing are RNA-RNA, DNA-DNA or RNA-DNA. Such standard
hybridization conditions are easily determined by one skilled in
the art according to well known formulae, wherein hybridization is
typically 10-20.degree. C. below the predicted or determined
T.sub.m with washes of higher stringency, if desired. As used
herein, the phrase "stringent hybridization conditions" refers to
conditions under which a probe, primer or oligonucleotide will
hybridize to its target sequence, but to no other sequences.
Stringent conditions are sequence-dependent and will be different
in different circumstances. Longer sequences hybridize specifically
at higher temperatures than shorter sequences. Generally, stringent
conditions are selected to be about 5.degree. C. lower than the
thermal melting point (T.sub.m) for the specific sequence at a
defined ionic strength and pH. The T.sub.m is the temperature
(under defined ionic strength, pH and nucleic acid concentration)
at which 50% of the probes complementary to the target sequence
hybridize to the target sequence at equilibrium. Since the target
sequences are generally present in excess, at T.sub.m, 50% of the
probes are occupied at equilibrium. Stringent conditions may also
be achieved with the addition of destabilizing agents, such as
formamide. Stringent conditions are known to those skilled in the
art. Preferably, the conditions are such that sequences at least
about 65%, 70%, 75%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%
homologous to each other typically remain hybridized to each
other.
[0050] As used herein, the term "nucleic acid molecule" is intended
to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules
(e.g., mRNA), analogs of the DNA or RNA generated using nucleotide
analogs, and derivatives, fragments and homologs thereof. The
nucleic acid molecule can be single-stranded or double-stranded,
but preferably is double-stranded DNA. An "isolated" nucleic acid
molecule is one that is separated from other nucleic acid molecules
that are present in the natural source of the nucleic acid.
Examples of isolated nucleic acid molecules include, but are not
limited to, recombinant DNA molecules contained in a vector,
recombinant DNA molecules maintained in a heterologous host cell,
partially or substantially purified nucleic acid molecules, and
synthetic DNA or RNA molecules. Preferably, an "isolated" nucleic
acid is free of sequences which naturally flank the nucleic acid
(i.e., sequences located at the 5' and 3' ends of the nucleic acid)
in the genomic DNA of the organism from which the nucleic acid is
derived. Moreover, an "isolated" nucleic acid molecule, such as a
cDNA molecule, can be substantially free of other cellular material
or culture medium when produced by recombinant techniques, or of
chemical precursors or other chemicals when chemically
synthesized.
[0051] As used herein, the term "oligonucleotide" refers to a
series of linked nucleotide residues, which oligonucleotide has a
sufficient number of nucleotide bases to be used in a PCR reaction.
A short oligonucleotide sequence may be based on, or designed from,
a genomic or cDNA sequence and is used to amplify, confirm, or
reveal the presence of an identical, similar or complementary DNA
or RNA in a particular cell or tissue. Oligonucleotides may be
chemically synthesized and may be used as primers or probes.
Oligonucleotide means any nucleotide of more than 3 bases in length
used to facilitate detection or identification of a target nucleic
acid, including probes and primers.
[0052] A DNA sequence is "operatively linked" to an expression
control sequence when the expression control sequence controls and
regulates the transcription and translation of that DNA sequence.
The term "operatively linked" includes having an appropriate start
signal (e.g., ATG or AUG) in front of the DNA sequence to be
expressed and maintaining the correct reading frame to permit
expression of the DNA sequence under the control of the expression
control sequence and production of the desired product encoded by
the DNA sequence. If a gene that one desires to insert into a
recombinant DNA molecule does not contain an appropriate start
signal, such a start signal can be inserted in front of the
gene.
[0053] "PCR" refers to a polymerase chain reaction, which is a
thermocyclic, polymerase-mediated, DNA amplification reaction. A
PCR typically includes template molecules, oligonucleotide primers
complementary to each strand of the template molecules, a
thermostable DNA polymerase, and deoxyribonucleotides, and involves
three distinct processes that are multiply repeated to effect the
amplification of the original nucleic acid. The three processes
(denaturation, hybridization, and primer extension) are often
performed at distinct temperatures, and in distinct temporal steps.
In many embodiments, however, the hybridization and primer
extension processes can be performed concurrently. The nucleotide
sample to be analyzed may be PCR amplification products provided
using the rapid cycling techniques described in U.S. Pat. No.
5,455,175.
[0054] A "polymerase" is an enzyme that catalyzes the sequential
addition of monomeric units to a polymeric chain, or links two or
more monomeric units to initiate a polymeric chain. In preferred
embodiments of this invention, the "polymerase" will work by adding
monomeric units whose identity is determined by and which is
complementary to a template molecule of a specific sequence. For
example, DNA polymerases such as DNA pol 1 and Taq polymerase add
deoxyribonucleotides to the 3' end of a polynucleotide chain in a
template-dependent manner, thereby synthesizing a nucleic acid that
is complementary to the template molecule.
[0055] "Primer" means an oligonucleotide comprised of more than
three deoxyribonucleotide used in amplification. Its exact length
will depend on many factors relating to the ultimate function and
use of the oligonucleotide primer, including temperature, source of
the primer and use of the method. The primer can occur naturally
(as a purified fragment or restriction digestion) or be produced
synthetically. The primer is capable of acting as an initiation
point for synthesis, when placed under conditions that induce
synthesis of a primer extension product complementary to a nucleic
acid strand. The conditions can include the presence of nucleotides
and an inducing agent such as a DNA polymerase at a suitable
temperature and annealing and extension times as well as the
appropriate buffer (pH, magnesium chloride (MgCl.sub.2) and
potassium chloride (KCl.sub.2) concentrations, and adjuncts). In
the preferred embodiment the primer is a single-stranded
oligodeoxyribonucleotide of sufficient length to prime the
synthesis of an extension product from a specific sequence in the
presence of an inducing agent. In the present application in the
preferred embodiment the oligonucleotide primer typically contains
about 10 to about 35 or more nucleotides, although it may contain
fewer nucleotides. More particularly, primers may contain about 15
to about 30 nucleotides, preferably primers may contain about 18 to
about 26 nucleotides. Sensitivity and specificity of the
oligonucleotide primers are determined by the primer length and
uniqueness of sequence within a given sample of a template DNA.
Primers that are too short, for example, less than 10 mer may show
non-specific binding to a wide variety of sequences in the genomic
DNA and thus are not very helpful. Each primer pair herein is
selected to be substantially complementary to the different strands
of each specific NTS region to which the primer pairs bind. Thus
one primer of each pair is sufficiently complementary to hybridize
with a part of the sequence in the sense strand and the other
primer of each pair is sufficiently complementary to hybridize with
a different part of the same repetitive sequence in the anti-sense
strand. The primer may be either single-stranded or double-stranded
and must be sufficiently long to prime the synthesis of the desired
extension product in the presence of the inducing agent. The exact
length of the primer will depend upon many factors, including
temperature and use of the method.
[0056] The primers herein are selected to be "substantially"
complementary to different strands of a particular target DNA
sequence. This means that the primers must be sufficiently
complementary to hybridize with their respective strands.
Therefore, the primer sequence need not reflect the exact sequence
of the template. For example, a non-complementary nucleotide
fragment may be attached to the 5' end of the primer, with the
remainder of the primer sequence being complementary to the strand.
Alternatively, non-complementary bases or longer sequences can be
interspersed into the primer, provided that the primer sequence has
sufficient complementarity with the sequence of the strand to
hybridize therewith and thereby form the template for the synthesis
of the extension product.
[0057] "Probes" refer to nucleic acid sequences of variable length,
preferably at least about 10 nucleotides (nt), but can be about 100
nt, or as many as about, e.g., 6,000 nt, depending on use. Probes
typically contain about 10 to about 35 or more nucleotides,
although it may contain fewer nucleotides. More particularly,
probes may contain about 15 to about 30 nucleotides, preferably
probes may contain about 18 to about 26 nucleotides. Probes are
used in the detection of identical, similar, or complementary
nucleic acid sequences by hybridization. Longer length probes are
usually obtained from a natural or recombinant source, are highly
specific and much slower to hybridize than oligomers. An
oligonucleotide sequence used as a detection probe may be labeled
with a detectable moiety. Various labeling moieties are known in
the art. Said moiety may, for example, either be a radioactive
compound, a detectable enzyme (e.g. horse radish peroxidase (HRP))
or any other moiety capable of generating a detectable signal such
as a calorimetric, fluorescent, chemiluminescent or
electrochemiluminescent signal. Preferred analysis systems wherein
said labels are used are electrochemiluminescence (ECL) based
analysis or enzyme linked gel assay (ELGA) based analysis. After
hybridization with a detectable amount of product, the detectable
moiety may be detected using known methods. Generally, the amount
of detectable moiety is detected and the measured amount is then
correlated to the amount of target DNA present. Preferably, the
methods of the present invention additionally comprise adding an
internal standard to the DNA amplification composition for
assessing the relative amounts of EBV present after amplification.
As already indicated above, and will be presented in the
experimental part of the description, both the sensitivity and
reliability of EBV mRNA detection is greatly improved using the
oligonucleotides according to the present invention when compared
to known oligonucleotides used in this art.
[0058] A "promoter sequence" is a DNA regulatory region capable of
binding RNA polymerase in a cell and initiating transcription of a
downstream (3' direction) coding sequence. For purposes of defining
the present invention, the promoter sequence is bounded at its 3'
terminus by the transcription initiation site and extends upstream
(5' direction) to include the minimum number of bases or elements
necessary to initiate transcription at levels detectable above
background. Within the promoter sequence will be found a
transcription initiation site (conveniently defined by mapping with
nuclease S1), as well as protein binding domains (consensus
sequences) responsible for the binding of RNA polymerase.
Eukaryotic promoters will often, but not always, contain "TATA"
boxes and "CAT" boxes. Prokaryotic promoters contain Shine-Dalgarno
sequences in addition to the -10 and -35 consensus sequences.
Promoter sequences can also be used to refer to analogous RNA
sequences or structures of similar function in RNA virus
replication and transcription.
[0059] A "thermocyclic reaction" is a multi-step reaction wherein
at least two steps are accomplished by changing the temperature of
the reaction.
[0060] A "thermostable polymerase" refers to a DNA or RNA
polymerase enzyme that can withstand extremely high temperatures,
such as those approaching 100.degree. C. Often, thermostable
polymerases are derived from organisms that live in extreme
temperatures, such as Thermus aquaticus. Examples of thermostable
polymerases include, Taq, Tth, Pfu, Vent, deep vent, UlTma, and
variations and derivatives thereof.
[0061] One embodiment of the present invention is directed to a
nucleic acid sequences (oligonucleotides) useful as primers and/or
probes in the detection of a Epstein-Barr virus in clinical
specimens. Also, the present invention is directed to a method of
detecting the presence of Epstein-Barr virus in a clinical specimen
wherein the oligonucleotides of the present invention may be used
to amplify target nucleic acid sequences of a Epstein-Barr virus
that may be contained within a clinical specimen, and/or to detect
the presence or absence of amplified target nucleic acid sequences
of the Epstein-Barr virus. Respective oligonucleotides may be used
to amplify and/or detect EBV and EBV nucleic acid sequences. By
using the oligonucleotides of the present invention and according
to the methods of the present invention, as few as one to ten
copies of the Epstein-Barr virus genome may be detected in the
presence of milligram quantities of extraneous DNA.
[0062] One embodiment of the present invention is directed to
EBV-specific oligonucleotides that can be used to amplify sequences
of EBV DNA, and to subsequently determine if amplification has
occurred, from DNA extracted from a clinical specimen. A pair of
EBV-specific DNA oligonucleotide primers are used to hybridize to
EBV genomic DNA that may be present in DNA extracted from a
clinical specimen, and to amplify the specific segment of genomic
DNA between the two flanking primers using enzymatic synthesis and
temperature cycling. Each pair of primers are designed to hybridize
only to the EBV DNA to which they have been synthesized to
complement; one to each strand of the double-stranded DNA. Thus,
the reaction is specific even in the presence of microgram
quantities of heterologous DNA. For the purposes of this
description, the primer derived from the sequence of the positive
strand of DNA will be referred to as the "positive (+) primer", and
the primer derived from the sequence of the negative strand will be
referred to as the "negative (-) primer".
[0063] In one embodiment, the present invention relates to a
composition for the detection of Epstein-Barr virus, consisting
essentially of at least one purified and isolated oligonucleotide
consisting of a nucleic acid sequence which complements and
specifically hybridizes to an Epstein-Barr virus nucleic acid
molecule, wherein said sequence is selected from the group
consisting of SEQ. ID. NO. 1, SEQ ID NO. 2, SEQ. ID. NO. 5, SEQ.
ID. NO. 6, and a nucleotide sequence which differs from SEQ. ID.
NO. 1, SEQ ID NO. 2, SEQ. ID. NO. 5, or SEQ. ID. NO. 6 by a one
base change or substitution therein.
[0064] An isolated and purified oligonucleotide primer pair for
enzymatic amplification of Epstein-Barr virus DNA, consisting
essentially of a pair of nucleic acid sequences which complement
and specifically hybridize to an Epstein-Barr virus nucleic acid
molecule, wherein said pair of nucleic acid sequences is selected
from the group consisting of SEQ. ID. NO. 3, SEQ. ID. NO. 4, SEQ.
ID. NO. 7, SEQ. ID. NO.8, and a nucleotide sequence which differs
from SEQ. ID. NO. 3, SEQ. ID. NO. 4, SEQ. ID. NO. 7, or SEQ. ID.
NO.8 by a one base change or substitution therein.
[0065] In another embodiment, the present invention relates to a
method of detecting the presence of Epstein Barr virus in a sample
comprising a) contacting the sample with the above-described
nucleic acid probe, under conditions such that hybridization
occurs, and b) detecting the presence of the probe bound to the DNA
segment.
[0066] In another embodiment, the present invention relates to a
method of detecting the presence of Epstein Barr virus in a sample
comprising a) contacting the sample with the above-described
nucleic acid probe, under conditions such that hybridization
occurs, and b) detecting the presence of the probe bound to the DNA
segment.
[0067] In another embodiment, the present invention relates to a
method of detecting the presence of Epstein Barr virus in a sample
comprising a) contacting the sample with the above-described
nucleic acid probe, under conditions such that hybridization
occurs, b) enzymatically amplifying a specific region of the EBV
nucleic acid molecules, and c) detecting the presence of the probe
bound to the DNA segment.
[0068] In another embodiment, the present invention relates to a
method of detecting the presence of Epstein Barr virus in a sample
comprising a) contacting the sample with the oligonucleotide primer
pair of SEQ. ID. NO. 1 and SEQ ID NO. 2 or the oligonucleotide pair
of SEQ. ID. NO. 5 and SEQ. ID. NO. 6 what under suitable conditions
permitting hybridization of the oligonucleotides to the nucleic
acid molecules of the EBV, b) enzymatically amplifying a specific
region of the EBV nucleic acid molecules using the oligonucleotide
pair of SEQ. ID. NO. 1 and SEQ ID NO. 2 or the oligonucleotide pair
of SEQ. ID. NO. 5 and SEQ. ID. NO. 6 to form nucleic acid
amplification products, c) contacting the amplified target
sequences from step be, is present, with hybridization probes
comprising the oligonucleotide pair of SEQ. ID. NO. 3 and SEQ. ID.
NO. 4 or the oligonucleotide pair of SEQ. ID. NO. 7 and SEQ. ID.
NO.8, labeled with a detectable moiety under suitable conditions
permitting hybridization of the labeled oligonucleotide probe to
amplified target sequences, and d) detecting the presence of
amplified target sequences by detecting the detectable moiety of
the labeled oligonucleotide probe hybridized to amplified target
sequences. In a preferred embodiment, prior to performing the above
method, the sample is treated to release nucleic acid molecules
from cells in the sample. In another preferred embodiment, the
presence of the amplified target sequences hybridized labeled
oligonucleotide probe correlates to the presence of Epstein Barr
virus in the sample.
[0069] In one embodiment, the method involves amplifying DNA
sequences from the EBNA2 region of the EBV genome.
[0070] Any one of the methods commercially available may accomplish
amplification of DNA. For example, the polymerase chain reaction
may be used to amplify the DNA. Once the primers have hybridized to
opposite strands of the target DNA, the temperature is raised to
permit replication of the specific segment of DNA across the region
between the two primers by a thermostable DNA polymerase. Then the
reaction is thermocycled so that at each cycle the amount of DNA
representing the sequences between the two primers is doubled, and
specific amplification of the EBV DNA sequences, if present,
results.
[0071] Further identification of the amplified DNA fragment, as
being derived from EBV DNA, may be accomplished by liquid
hybridization. This method utilizes one or more oligonucleotides
labeled with detectable moiety as probes to specifically hybridize
to the amplified segment of EBV DNA. Detection of the presence of
sequence-specific amplified EBV DNA may be accomplished by
simultaneous detection of the complex comprising the labeled
oligonucleotide hybridized to the sequence-specific amplified EBV
DNA ("amplified target sequences") with respect to the DNA
amplification. Detection of the presence of sequence-specific
amplified EBV DNA may also be accomplished using a gel retardation
assay with subsequent detection of the complex comprising the
labeled oligonucleotide hybridized to the sequence-specific
amplified EBV DNA.
[0072] In such a enzymatic amplification reaction hybridization
system of EBV detection, a clinical specimen of blood, CSF,
amniotic fluid, urine, body secretions, or other body fluid is
subjected to a DNA extraction procedure. High molecular weight DNA,
including Epstein-Barr virus DNA, may be purified from blood cells,
tissue cells, or virus particles (collectively referred to herein
as "cells") contained in the clinical specimen using proteinase
(proteinase K) extraction and ethanol precipitation. DNA may be
extracted from a clinical specimen using other methods known in the
art. Then, for example, the DNA extracted from the clinical
specimen is enzymatically amplified in the polymerase chain
reaction using EBV-specific oligonucleotides (SEQ ID NO:1 & SEQ
ID NO:2; or SEQ ID NO:5 & SEQ ID NO:6) as primer pairs.
Following amplification, EBV-specific oligonucleotides (SEQ ID NO:3
or SEQ ID NO:4, for use with SEQ ID NOs:1 & 2; or SEQ ID NO:7
or SEQ ID NO:8, for use with SEQ ID NOs:3 & 4) labeled with an
appropriate detectable label are hybridized to the amplified target
sequences, if present.
[0073] The contents of the hybridization reaction are then analyzed
for detection of the sequence-specific amplified EBV DNA, if
present in the DNA extracted from the clinical specimen. Thus, the
oligonucleotides of the present invention have commercial
applications in diagnostic kits for the detection of EBV DNA in
clinical specimens.
[0074] The test samples suitable for nucleic acid probing methods
of the present invention include, for example, cells or nucleic
acid extracts of cells, or biological fluids. The sample used in
the above-described methods will vary based on the assay format,
the detection method and the nature of the tissues, cells or
extracts to be assayed. Methods for preparing nucleic acid extracts
of cells are well known in the art and can be readily adapted in
order to obtain a sample that is compatible with the method
utilized.
[0075] In a related embodiment of the present invention, the
EBV-specific oligonucleotides may be used to amplify and detect EBV
DNA from DNA extracted from a clinical specimen. In this
embodiment, the oligonucleotides used as primers may be labeled
directly with detectable moiety, or synthesized to incorporate the
label molecule. Depending on the label molecule used, the
amplification products can then be detected, for example, after
binding onto an affinity matrix, using isotopic or calorimetric
detection.
[0076] In a preferred embodiment of this invention, cyclic
polymerase-mediated reactions are performed. In certain embodiments
of this invention, these processes are accomplished by changing the
temperature of the solution containing the templates, primers, and
polymerase. In such embodiments, the denaturation step is typically
accomplished by shifting the temperature of the solution to a
temperature sufficiently high to denature the template. In some
embodiments, the hybridization step and the extension step are
performed at different temperatures. In other embodiments, however,
the hybridization and extension steps are performed concurrently,
at a single temperature.
[0077] In some embodiments, the cyclic polymerase-mediated reaction
is performed at a single temperature, and the different processes
are accomplished by changing non-thermal properties of the
reaction. For example, the denaturation step can be accomplished by
incubating the template molecules with a basic solution or other
denaturing solution.
[0078] In preferred embodiments, the percentage of template
molecules that are duplicated in the cycle steps is e.g. 90%, 70%,
50%, 30%, or less. Such cycles may be as short as 8-10, 6, 5, 4.5,
4, 2, 1, 0.5 minutes or less. In certain embodiments, the reaction
comprises 2, 5, 10, 15, 20, 30, 40, 50, or more cycles.
[0079] Typically, the reactions described herein are repeated until
a detectable amount of product is generated. Often, such detectable
amounts of product are between about 10 ng and about 100 ng,
although larger quantities, e.g. 200 ng, 500 ng, 1 mg or more can
also, of course, be detected. In terms of concentration, the amount
of detectable product can be from about 0.01 pmol, 0.1 pmol, 1
pmol, 10 pmol, or more.
[0080] Oligonucleotides for use as primers, e.g., in PCR or
non-thermal amplification reactions, are typically synthesized
chemically according to the solid phase phosphoramidite triester
method, e.g., using an automated synthesizer. Oligonucleotides can
also be custom made and ordered from a variety of commercial
sources known to persons of skill. Purification of
oligonucleotides, where necessary, is typically performed by either
native acrylamide gel electrophoresis or by anion-exchange
HPLC.
[0081] Any of a variety of polymerases can be used in the present
invention. For thermocyclic reactions, the polymerases are
thermostable polymerases such as Taq, KlenTaq, Stoffel Fragment,
Deep Vent, Tth, Pfu, Vent, and UlTma, each of which are readily
available from commercial sources. Similarly, guidance for the use
of each of these enzymes can be readily found in any of a number of
protocols found in guides, product literature, and other
sources.
[0082] For non-thermocyclic reactions, and in certain thermocyclic
reactions, the polymerase will often be one of many polymerases
commonly used in the field, and commercially available, such as DNA
pol 1, Klenow fragment, T7 DNA polymerase, and T4 DNA polymerase.
Guidance for the use of such polymerases can readily be found in
product literature and in general molecular biology guides.
[0083] Those of skill in the art are aware of the variety of
nucleotides available for use in the present reaction. Typically,
the nucleotides will consist at least in part of deoxynucleotide
triphosphates (dNTPs), which are readily commercially available.
Parameters for optimal use of dNTPs are also known to those of
skill, and are described in the literature. In addition, a large
number of nucleotide derivatives are known to those of skill and
can be used in the present reaction. Such derivatives include
fluorescently labeled nucleotides, allowing the detection of the
product including such labeled nucleotides, as described below.
Also included in this group are nucleotides that allow the
sequencing of nucleic acids including such nucleotides, such as
dideoxynucleotides and boronated nuclease-resistant nucleotides, as
described below. Other nucleotide analogs include nucleotides with
bromo-, iodo-, or other modifying groups, which groups affect
numerous properties of resulting nucleic acids including their
antigenicity, their replicatability, their melting temperatures,
their binding properties, etc. In addition, certain nucleotides
include reactive side groups, such as sulfhydryl groups, amino
groups, N-hydroxysuccinimidyl groups, that allow the further
modification of nucleic acids comprising them.
[0084] An oligonucleotide sequence used as a detection probe may be
labeled with a detectable moiety. Various labeling moieties are
known in the art. Said moiety may, for example, either be a
radioactive compound, a detectable enzyme (e.g. horse radish
peroxidase (HRP)) or any other moiety capable of generating a
detectable signal such as a calorimetric, fluorescent,
chemiluminescent or electrochemiluminescent signal. Preferred
analysis systems wherein said labels are used are
electrochemiluminescence (ECL) based analysis or enzyme linked gel
assay (ELGA) based analysis.
[0085] In one class of embodiments of this invention, a detectable
label is incorporated into a nucleic acid during at least one cycle
of the reaction. Spectroscopic, photochemical, biochemical,
immunochemical, electrical, optical or chemical means can detect
such labels. Useful labels in the present invention include
fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red,
rhodamine, and the like), radiolabels (e.g., .sup.3H, .sup.125I,
.sup.35S, .sup.14C, .sup.32P, etc.), enzymes (e.g. horse-radish
peroxidase, alkaline phosphatase etc.) calorimetric labels such as
colloidal gold or colored glass or plastic (e.g. polystyrene,
polypropylene, latex, etc.) beads. The label is coupled directly or
indirectly to a component of the assay according to methods well
known in the art. As indicated above, a wide variety of labels are
used, with the choice of label depending on sensitivity required,
ease of conjugation with the compound, stability requirements,
available instrumentation, and disposal provisions. Non-radioactive
labels are often attached by indirect means. Polymerases can also
incorporate fluorescent nucleotides during synthesis of nucleic
acids.
[0086] Reagents allowing the sequencing of reaction products can be
utilized herein. For example, chain-terminating nucleotides will
often be incorporated into a reaction product during one or more
cycles of a reaction. Commercial kits containing the reagents most
typically used for these methods of DNA sequencing are available
and widely used. PCR exonuclease digestion methods for DNA
sequencing can also be used.
[0087] Typically, the amplification sequence is serially diluted
and then quantitatively amplified via the DNA Tag polymerase using
a suitable PCR amplification technique. In PCR, annealing of the
primers to the amplification sequence is generally carried out at
about 37-50.degree. C.; extension of the primer sequence by Taq
polymerase in the presence of nucleoside triphosphates is carried
out at about 70-75.degree. C.; and the denaturing step to release
the extended primer is carried out at about 90-95.degree. C. In the
two temperature PCR technique, the annealing and extension steps
may both be carried at about 60-65.degree. C., thus reducing the
length of each amplification cycle and resulting in a shorter assay
time.
[0088] Polymerase chain reactions (PCR) are generally carried out
in about 25-50 .mu.l samples containing 0.01 to 1.0 ng of template
amplification sequence, 10 to 100 pmol of each generic primer, 1.5
units of Tag DNA polymerase (Promega Corp.), 0.2 mM DATP, 0.2 mM
dCTP, 0.2 mM dGTP, 0.2 mM dTTP, 15 mM MgCl.sub.2, 10 mM Tris-HCl
(pH 9.0), 50 mM KCl, 1 .mu.g/ml gelatin, and 10 .mu.l/ml Triton
X-100 (Saiki, 1988). Reactions are incubated at 94.degree. C. for 1
minute, about 37 to 55.degree. C. for 2 minutes (depending on the
identity of the primers), and about 72.degree. C. for about 3
minutes and repeated for about 5-40, cycles. A two temperature PCR
technique differs from the above only in carrying out the
annealing/extension steps at a single temperature, e.g., about
60-65.degree. C. for about 5 minutes, rather than at two
temperatures.
[0089] Quantitative methods employing PCR are known. The main
constraint in obtaining accurate quantitative data is inherent in
the amplification process. Because amplification is (at least
initially) an exponential process, small difference in any of the
variables that control the reaction rate will dramatically affect
the yield of the PCR product. These variables include the
concentration of polymerase, dNTPs, Mg.sup.2, DNA and primers,
annealing, extension and denaturing temperatures; cycle length and
cycle number; ramping times; rate of "primer-dimer" formation and
the presence of contaminating DNA.
[0090] Quantitation of the original target nucleic acid in the
sample may be performed by a competitive PCR method to
quantitatively amplify the amplification sequence, as provided,
e.g., in Sambrook et al., Molecular Cloning--A Laboratory Manual,
2d Edition, Cold Spring Harbor Laboratory, 1989.
[0091] The invention comprises methods for quantitatively analyzing
either an amplifiable or a self-replicating system in such a way
that the amount of amplification or self-replication product is
measured continuously. Continuous measurement in a PCR reaction,
for example, may also mean that measurements are performed once
each cycle. The method of the present invention is especially
applicable for embodiments, wherein during one phase of the
amplification reaction or self-replication (usually starting from
the beginning or alternatively after an initial lag phase) the
amount of the target product increases progressively. Moreover, the
method is applicable for embodiments wherein after said exponential
phase, the rate of amplification decreases.
[0092] Co-amplification of a competitive substrate is a technique
used to quantitate sample. The competitive substrate functions as
an internal standard. The strategy involves co-amplification of a
competitive template that uses the same primers as those of the
target cDNA but can be distinguished from the target cDNA after
amplification. Since a change in any of the variables previously
listed will affect the yield of the competitive template equally,
relative ratios of the two should be preserved with amplification.
The use of real time fluorescent monitoring of nucleic acid
reactions has been described in U.S. Pat. No. 5,455,175.
[0093] Another embodiment of the present invention is directed to
EBV-specific oligonucleotides that can be used to amplify sequences
of EBV DNA, and to subsequently determine if amplification has
occurred, from DNA extracted from a clinical specimen. A pair of
EBV-specific DNA oligonucleotide primers are used to hybridize to
EBV genomic DNA that may be present in DNA extracted from a
clinical specimen, and to amplify the specific segment of genomic
DNA between the two flanking primers using enzymatic synthesis and
temperature cycling. Each pair of primers are designed to hybridize
only to the EBV DNA to which they have been synthesized to
complement; one to each strand of the double-stranded DNA. The
region to which the primers have been synthesized to complement is
conserved in EBV. Thus, the reaction is specific even in the
presence of microgram quantities of heterologous DNA.
[0094] A nucleic acid molecule of the present invention, e.g., a
nucleic acid molecule having the nucleotide sequence of SEQ ID
NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID
NO:6, SEQ ID NO:7 or SEQ ID NO:8, or a complement thereof, can be
isolated using standard molecular biology techniques and the
sequence information provided herein. Using all or a portion of the
nucleic acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ
ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, as a
hybridization probe, nucleic acid sequences can be isolated using
standard hybridization and cloning techniques. Furthermore,
oligonucleotides can be prepared by standard synthetic techniques,
e.g., using an automated DNA synthesizer.
[0095] In another embodiment, an isolated nucleic acid molecule of
the invention comprises a nucleic acid molecule that is a
complement of the nucleotide sequence shown in SEQ ID NO:1, SEQ ID
NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8 or a portion of this nucleotide sequence. A
nucleic acid molecule that is complementary to the nucleotide
sequence shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID
NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, is one
that is sufficiently complementary to the nucleotide sequence shown
in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5,
SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8 that it can bind with few
or no mismatches to the nucleotide sequence shown in SEQ ID NO:1,
SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6,
SEQ ID NO:7 or SEQ ID NO:8, thereby forming a stable duplex.
[0096] A nucleic acid molecule of the invention may include only a
fragment of the nucleic acid sequence of SEQ ID NO:1, SEQ ID NO:2,
SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or
SEQ ID NO:8. Fragments provided herein are defined as sequences of
at least 6 (contiguous) nucleic acids, a length sufficient to allow
for specific hybridization of nucleic acids, and are at most some
portion less than a full-length sequence. Fragments may be derived
from any contiguous portion of a nucleic acid sequence of choice.
Derivatives are nucleic acid sequences formed from the native
compounds either directly or by modification or partial
substitution. Analogs are nucleic acid sequences that have a
structure similar to, but not identical to, the native compound but
differ from it in respect to certain components or side chains.
Analogs may be synthetic or from a different evolutionary origin
and may have a similar or opposite metabolic activity compared to
wild type.
[0097] Derivatives and analogs may be full length or other than
full length, if the derivative or analog contains a modified
nucleic acid or amino acid, as described below. Derivatives or
analogs of the nucleic acids of the invention include, but are not
limited to, molecules comprising regions that are substantially
homologous to the nucleic acids of the invention, in various
embodiments, by at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%,
98%, or even 99% identity (with a preferred identity of 80-99%)
over a nucleic acid sequence of identical size or when compared to
an aligned sequence in which the alignment is done by a computer
homology program known in the art. Derivatives or analogs of the
nucleic acids of the invention also include, but are not limited
to, molecules comprising regions that are substantially homologous
to the nucleic acids of the invention, in various embodiments, by
at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or even 99%
identity (with a preferred identity of 80-99%) under stringent,
moderately stringent, or low stringent conditions.
[0098] The nucleotide sequence of probes and primers typically
comprises a substantially purified oligonucleotide. The
oligonucleotide typically comprises a region of nucleotide sequence
that hybridizes under stringent conditions to at least about 6, 9,
12, 25, or more consecutive sense strand nucleotide sequence of SEQ
ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID
NO:6, SEQ ID NO:7 or SEQ ID NO:8, or an anti-sense strand
nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ
ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or
of a naturally occurring mutant of SEQ ID NO:1, SEQ ID NO:2, SEQ ID
NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID
NO:8.
[0099] In various embodiments, the probe further comprises a label
group attached thereto. Such probes can be used as a part of a
diagnostic test kit for identifying EBV infection, such as by
measuring a level of an EBV nucleic acid in a sample of cells e.g.,
detecting EBV DNA levels in a clinical specimen of blood,
cerebral-spinal fluid ("CSF"), saliva, amniotic fluid, urine, body
secretions, or other body fluid and tissues.
[0100] The invention further encompasses nucleic acid molecules
that differ from the nucleotide sequences shown in SEQ ID NO:1, SEQ
ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8, due to the degeneracy of the genetic code.
[0101] In addition to the nucleotide sequence shown in SEQ ID NO:1,
SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6,
SEQ ID NO:7 or SEQ ID NO:8, it will be appreciated by those skilled
in the art that DNA sequence polymorphisms in the EBV DNA may exist
within a population. Such natural allelic variations can typically
result in about 1-5% variance in the nucleotide sequence of the
gene. Any and all such nucleotide variations are intended to be
within the scope of the invention.
[0102] Moreover, nucleic acid molecules that differ from the
sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ
ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, are intended to
be within the scope of the invention. Nucleic acid molecules
corresponding to natural allelic variants and homologues of the
DNAs of the invention can be isolated based on their homology to
the nucleic acids disclosed herein using standard hybridization
techniques under stringent hybridization conditions. Preferably,
such variations will differ from the sequence of SEQ ID NO:1, SEQ
ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID
NO:7 or SEQ ID NO:8, by only one nucleotide.
[0103] Accordingly, in another embodiment, an isolated nucleic acid
molecule of the invention is at least 6 nucleotides in length and
hybridizes under stringent conditions to the nucleic acid molecule
comprising the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ
ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ
ID NO:8.
[0104] Homologs (i.e., nucleic acids derived from other species) or
other related sequences (e.g., paralogs) can be obtained under
conditions of standard or stringent hybridization conditions with
all or a portion of the particular sequence as a probe using
methods well known in the art for nucleic acid hybridization and
cloning.
[0105] In another embodiment, a nucleic acid sequence that is
hybridizable to the nucleic acid molecule comprising the nucleotide
sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ
ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8, or fragments,
analogs or derivatives thereof, under conditions of standard or
stringent hybridization conditions is provided.
[0106] In addition to naturally-occurring allelic variants of the
nucleotide sequence, the skilled artisan will further appreciate
that changes can be introduced by mutation into the nucleotide
sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ
ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8.
[0107] In one embodiment, the isolated nucleic acid molecule
comprises a nucleotide sequence at least about 75% homologous to
the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3,
SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8.
Preferably, the nucleic acid is at least about 80% homologous to
the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3,
SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8,
more preferably at least about 90%, 95%, 96%, 97%, 98%, and most
preferably at least about 99% homologous to the nucleotide sequence
of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5,
SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8.
[0108] As already indicated above, and will be presented in the
experimental part of the description, both the sensitivity and
reliability of EBV mRNA detection is greatly improved using the
oligonucleotides according to the present invention when compared
to known oligonucleotides used in this art.
[0109] It is understood that oligonucleotides consisting of the
sequences of the present invention may contain minor deletions,
additions and/or substitutions of nucleic acid bases, to the extent
that such alterations do not negatively affect the yield or product
obtained to a significant degree.
[0110] Test kits for the detection of EBV in clinical samples are
also part of the present invention. A test kit according to the
invention may comprise a pair of oligonucleotides according to the
invention and a probe comprising an oligonucleotide according to
the invention. Such a test kit may additionally comprise suitable
amplification reagents such as DNA and or RNA polymerases and
mononucleotides. Test kits that can be used with the method
according to the invention may comprise the oligonucleotides
according to the invention for the amplification and subsequent
detection of EBV mRNA. A preferred embodiment for the test kit
comprises the oligonucleotides: SEQ ID NO:1 & SEQ ID NO:2; or
SEQ ID NO:5 & SEQ ID NO:6 as primer pairs for the
amplification, and oligonucleotides SEQ ID NO:3 or SEQ ID NO:4, for
use with SEQ ID NOs:1 & 2; or SEQ ID NO:7 or SEQ ID NO:8, for
use with SEQ ID NOs:3 & 4, provided with a detectable label, as
probes.
[0111] A diagnostic test kit for detection of EBV according to the
compositions and methods of the present invention may include, in
separate packaging, a lysing buffer for lysing cells contained in
the specimen; at least one oligonucleotide primer pair (SEQ ID NO:1
& SEQ ID NO:2; or SEQ ID NO:5 & SEQ ID NO:6; or both SEQ ID
NO:1 & SEQ ID NO:2; and SEQ ID NO:5 & SEQ ID NO:6); enzyme
amplification reaction components such as dNTPs, reaction buffer,
and/or amplifying enzyme; and at least one oligonucleotide probe
labeled with a detectable moiety (SEQ ID NO:3 or SEQ ID NO:4, for
use with SEQ ID NOs:1 & 2; or SEQ ID NO:7 or SEQ ID NO:8, for
use with SEQ ID NOs:3 & 4), or various combinations
thereof.
[0112] The present invention further provides nucleic acid
detection kits, including arrays or microarrays of nucleic acid
molecules that are based on one or more of the sequences provided
in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5,
SEQ ID NO:6, SEQ ID NO:7 and SEQ ID NO:8. As used herein "Arrays"
or "Microarrays" refers to an array of distinct polynucleotides or
oligonucleotides synthesized on a substrate, such as paper, nylon
or other type of membrane, filter, chip, glass slide, or any other
suitable solid support. In one embodiment, the microarray is
prepared and used according to the methods described in U.S. Pat.
No. 5,837,832, Chee et al., In other embodiments, such arrays are
produced by the methods described by Brown et al., U.S. Pat. No.
5,807,522. The oligonucleotides are generally about 5-35
nucleotides in length, preferably about 10-30 nucleotides in length
and more preferably about 18-26 nucleotides in length. For a
certain type of microarray or detection kit, it may be preferable
to use oligonucleotides that are only 4-18 nucleotides in
length.
[0113] It should be understood that while the invention has been
described in detail herein, the examples were for illustrative
purposes only. Other modifications of the embodiments of the
present invention that are obvious to those of ordinary skill in
the art of molecular biology, medical diagnostics, and related
disciplines are intended to be within the scope of the appended
claims.
[0114] The invention will be further illustrated in the following
non-limiting examples.
EXAMPLES
[0115] The invention is further illustrated in the following
examples, which are not intended to be in any way limiting to the
scope of the invention as claimed.
EXPERIMENTAL
[0116] Quantitative EBV Assay for the LIGHTCYCLER.RTM.
[0117] The present invention, a quantitative EBV assay, is capable
of amplifying EBV genomic DNA from samples and can detect down to a
level of 3-4 copies of EBV genome per test sample.
[0118] The results [not shown] typically show a range of detectable
EBV DNA levels using a series of sample dilutions from a known
source of EBV virus (EBV B95-8, Advanced Biotechnologies
Incorporated Columbia Md.). Also included in the test samples is
one patient sample showing >3,000 copies of EBV.
[0119] These levels are followed at biweekly intervals for 3 months
after documentation of the initial infection, then monthly
intervals for 1 year followed by yearly checks. If at anytime
during this time course there is reactivation of the EBV infection
the blood monitoring may be increased in frequency.
[0120] During the past year 204 patient blood samples from patients
were evaluated to determine the EBV copy number based on the assay
described herein. The blood samples were obtained from a mixture of
pediatric age patients, some of which were immunocompromised,
including organ transplant patients, oncology patients undergoing
cytotoxic chemotherapy, patients with inborn genetic defects in
their immune system, and at high risk for EBV infection and others
who are immunocompetent. All blood samples were submitted at the
request of the attending physician for diagnostic EBV PCR studies
(Diasorin/Incstar, Stillwater, Minn.). Samples were split, and run
in parallel to compare the results of the qualitative Diasorin
assay with the present method. A high degree of correlation was
found when comparing the two assays for validation purposes. The
tables I and II represent the total number of patient samples that
were validated against each other.
1 TABLE 1 Quantitative Date of Sample Results Patient I Feb. 18,
2000 0.00 Feb. 24, 2000 0* Mar. 8, 2000 404.00 Mar. 15, 2000
36740.00 Apr. 5, 2000 120.00 Apr. 11, 2000 0.00 Apr. 17, 2000 0.00
Jun. 6, 2000 3000.00 Jun. 10, 2000 63040.00 Jun. 14, 2000 3920.00
Patient II Aug. 23, 2000 5640.00 Aug. 24, 2000 2320.00 Aug. 30,
2000 1230.00 Sep. 7, 2000 40.00 Apr. 11, 2000 0.00 Apr. 17, 2000
0.00 Jun. 6, 2000 3000.00 Jun. 10, 2000 63040.00 Jun. 14, 2000
3920.00 Patient III Apr. 11, 2000 0.00 Apr. 21, 2000 0.00 May 4,
2000 327.30 May 22, 2000 1677.00 May 27, 2000 1837.00
[0121]
2 TABLE II Positive Negative Equivocal Qualitative Results 125 66
14* (Diasorin Assay) Quantitative Results 129/6 75/8 0 *O.D.
reading <0.600
[0122] Patient results listed in the equivocal column in the
qualitative (Diasorin/Incstar, Stillwater, Minn.) assay are based
on results that were greater than the negative O.D. cutoff point
(0.50) but less than 0.60 reading. No PCR inhibition was observed
in samples with negative test results. To evaluate the specificity
of the assay, a panel of 20 samples known to be positive for a
variety of viral pathogens was also evaluated by the present assay.
These samples included the following viral pathogens: adenovirus,
cytomegalovirus, herpes simplex, enterovirus, and parvovirus.
[0123] None of these samples showed cross reaction with the present
assay described below.
[0124] Reproducibility
[0125] The performance of the assay at different concentration
ranges was determined using EBV B95-8, (Advanced Biotechnologies
Incorporated Columbia Md.). Ten identical samples with 10,000
copies and ten identical samples with 5,000 copies were analyzed
simultaneously. The target sequence was detected with specific
hybridization probes as described below. The results show that
5,000 and 10,000 copies could be clearly differentiated and the
coefficient of variation of less than 7.5% was obtained for a
series of identical samples with less than 100 copies.
[0126] Listed above are the results of assays using the
quantitative EBV assay described herein. All three examples
represent analyses performed sequentially over a period of time, as
indicated in the graphs, on patients who were immunosuppressed, and
at high risk for developing EBV lymphoproliferative disease.
Patient I was a bone marrow transplant patient who exhibited a
bimodal elevation of EBV copy numbers in the peripheral blood with
a range from 0.0 to more than 63,000 copies over a 4-month period.
These bimodal peak levels corresponded with two periods of
immunosuppressive therapy for graft versus host disease during
which time the patient was highly immunosuppressed.
[0127] During the interval between peak levels, immunosuppressive
therapy was withdrawn and associated with a drop in EBV copy
numbers. Patient II represents an immunosuppressed bone marrow
transplant patient who was initially monitored during an episode of
biopsy proven active EBV lymphoproliferative disease. Therapeutic
intervention to control the EBV infection and restore
immunocompetence was instituted which was associated with the fall
in EBV copy levels as shown in the graph from an initially high
level of greater than 5,000 to less than 50 copies. Patient III
shows a rise in EBV copy number from a baseline of 0.0 to more than
1800 during a 6 week time period. This patient was a liver
transplant recipient who during the time period illustrated in
graph number III was being treated aggressively for transplant
rejection with high dose immunosuppression.
[0128] Materials for Assay
[0129] Equipment: LIGHTCYCLER.RTM. Instrument (Roche Diagnostics,
Mannheim, Germany) with Oligo Software.
[0130] Reagents: Amplification Primers (University of Cincinnati
DNA Core Facility); Hybridization Probes (Genset); Qiagen Digestion
Kit (Qiagen); FastStart LIGHTCYCLER.RTM. DNA Master Hybridization
Probes; LIGHTCYCLER.RTM. Control Kit DNA; Advanced Biotechnologies
Inc (EBV viral DNA).
[0131] Assay Procedure
[0132] Viral DNA was prepared, using the Qiagen whole blood
digestion kit according to the manufacture's instructions. Starting
with 200 .mu.l of whole blood, 20 .mu.l of Proteinase K (20 mg/ml)
was added then 200 .mu.l of a lysis buffer. Samples were then
incubated for about 10 minutes at about 56.degree. C. The samples
are then ran over a spin column, washed and then eluted with a
Tris-EDTA solution. The eluted product was used directly in a PCR
reaction without any further treatment. From 1 ml of whole blood
were acquired about 10.0 .mu.g of genomic DNA. The LIGHTCYCLER.RTM.
reaction runs with 100 ng of genomic DNA, which is approximately 2
.mu.l of digested sample.
[0133] The EBV genome is a 170-kilobase linear DNA molecule that
consists of largely unique DNA domains (U1, U2, U3, U4, and U5), as
shown in FIG. 1, with internal tandem direct repeats (IR1, IR2,
IR3, IR4), and terminal repeats (TR). In latently infected cells,
the complete viral genome persists as episomes or integrated DNA.
The expression of viral genome is limited. However, at least three
sites on the viral genome are characteristically transcribed:
[0134] I. IR1 into U2
[0135] II. U3 through IR3 into U4
[0136] III. From U5
[0137] This protocol is set up to amplify the EBNA 2 region using
primers shown in Table III.
3 TABLE III Position Length GC (%) Tm (C) Primers
GGCTGGTGTCACCTGTTA 90030:90049 18 55 50 (SEQ. ID. NO. 1)
CCTTAGGAGGAACAAGTCCC 90249:90269 20 55 50 (SEQ. ID. NO. 2) Product
90030:90269 239 Hybridization Probes GGTGGAGGGCTGAGTGTCTCTGGGT-F
red 640 90114:90139 25 64 71.8 (SEQ. ID. NO. 3)
GAACTGGGTCTCAGTGACATGGAAGA-p 90142:90167 26 50 66.9 (SEQ. ID. NO.
4)
[0138] Other sequences that may be used include:
4 Primers: (sense) AGGGATGCCTGGACACAAGA (SEQ. ID. NO. 5)
(antisense) ATTGCCACCACCAGCAGCACCA (SEQ. ID. NO. 6) Probes (1)
CATCTGCTATGCGAATGCTTTG (SEQ. ID. NO. 7) (2) GCTAATTATATTGTAAGACA
(SEQ. ID. NO. 8)
[0139] LIGHTCYCLER PCR
[0140] The master mix shown in Table IV was used for amplification
and hybridization probe-based detection of the Epstein Barr
specific amplicon.
5TABLE IV Epstein Barr Virus Master Mix Volume Final (.mu.l)
concentration Sterile water 4.9 MgCl.sub.2 stock solution 2.4 4.0
mM Primer 1 1.4 0.5 .mu.M Primer 2 1.6 0.5 .mu.M Red Probe 2.5 0.4
.mu.M Flour. Probe 3.2 0.175 .mu.M LIGHTCYCLER 2 1X enzyme
[0141] To complete the amplification mixtures, 18 .mu.l of master
mix and 21 (100 ng) of the corresponding template DNA preparation
were added to each capillary. After a short centrifugation, the
sealed capillaries were placed into the LIGHTCYCLER.RTM. rotor.
[0142] The negative PCR control sample was prepared by replacing
the DNA template with PCR grade water. Another negative control
that was used was genomic DNA that was provided with the
.beta.-globulin kit. A positive control sample was purchased from
Advanced Biotech.
[0143] The following PCR protocol was used for amplification and
Hybridization probe-based detection of the Epstein Barr specific
amplicons using the parameters of Table V.
[0144] Denaturation for 10 minutes at 95.degree. C.
[0145] Amplification
6TABLE V PARAMETER VALUE Cycles Quantification Type Segment 1
Segment 2 Segment 3 Target temperature (.degree. C.) 95 52 72
Incubation time (s) 10 15 10 temperature transition rate (C./s) 20
20 20 Acquisition mode None Single None Gains F1-1, F2-15,
F3-30
[0146] Cooling for 2 minutes at 40.degree. C.
[0147] Copy Number Calculation
[0148] The amplification curves were obtained by the previous
procedure for single color detection using LIGHTCYCLER.RTM.--Red
640 as acceptor flourophore. The LIGHTCYCLER.RTM. software allows
the full log-linear region of the amplification. To minimize
extrapolation error the log lines are extrapolated to the noise
band line which define the beginning of the log-linear phase. A
standard curve is constructed by plotting the crossing points
against the common logarithm of standards copy number. The copy
number of unknown samples is calculated by interpolation of the
standard curve.
[0149] The development and implementation of this assay can provide
a highly sensitive, accurate, more rapid quantitative PCR assay to
detect EBV copies in this population of patients who are at high
risk to develop serious and costly medical complications and
hopefully allow for better clinical management of these patients by
earlier recognition of their infection status.
[0150] The present assay has a broad dynamic range of detection
from <10 to 10,000,000 copies of EBV DNA, is less labor
intensive requiring only one reaction tube for the EBV
determination, and has a rapid turn around time with assays that
are completed, including amplification, probe specific
hybridization, and calculation of copy number in less than 1 hour.
The methods of the present invention may be adapted to automated
systems such as the MagnaPure system by Roche.
OTHER EMBODIMENTS
[0151] While the invention has been described in conjunction with
the detailed description thereof, the foregoing description is
intended to illustrate and not limit the scope of the invention,
which is defined by the scope of the appended claims. Other
aspects, advantages, and modifications are within the scope of the
following claims.
Sequence CWU 1
1
8 1 18 DNA Human herpesvirus 4 1 ggctggtgtc acctgtta 18 2 20 DNA
Human herpesvirus 4 2 ccttaggagg aacaagtccc 20 3 25 DNA Human
herpesvirus 4 3 ggtggagggc tgagtgtctc tgggt 25 4 26 DNA Human
herpesvirus 4 4 gaactgggtc tcagtgacat ggaaga 26 5 20 DNA Human
herpesvirus 4 5 agggatgcct ggacacaaga 20 6 22 DNA Human herpesvirus
4 6 attgccacca ccagcagcac ca 22 7 22 DNA Human herpesvirus 4 7
catctgctat gcgaatgctt tg 22 8 20 DNA Human herpesvirus 4 8
gctaattata ttgtaagaca 20
* * * * *