Detection of HIV-1 DNA

Abstract

The determination of the nucleotide sequence of HTLV-III DNA; identification, isolation and expression of HTLV-III sequences which encode immunoreactive polypeptides by recombinant,DNA methods and production of viral RNA are disclosed. Such polypeptides can be employed in immunoassays to detect HTLV-III.

Description

RELATED APPLICATION

[0001] This application is a continuation-in-part of U.S. application Ser. No. 659,339, filed Oct. 10, 1984.

TECHNICAL FIELDS

[0002] This invention is in the fields of molecular biology and virology and in particular relates to human T cell leukemia virus--type III (HTLV-III).

BACKGROUND

[0003] The term human T cell leukemia-lymphoma virus (HTLV) refers to a unique family of T cell tropic retroviruses. These viruses play an important role in the pathogenesis of certain T cell neoplasms. There are presently three known types of HTLVs. One subgroup of the family, HTLV-type I (HTLV-I), is linked to the cause of adult T-cell leukemia-lymphoma (ATLL) that occurs in certain regions of Japan, the Caribbean and Africa. HTLV-type II (HTLV-II) has been isolated from a patient with a T-cell variant of hairy cell leukemia. M. Popovic et al., Detection, Isolation, and Continuous Production of Cytopathic Retroviruses (HTLV-III) from Patients with AIDS and Pre-AIDS. Science, 224:497-500 (1984).

[0004] HTLV-type III (HTLV-III) has been isolated from many patients with acquired immunodeficiency syndrome (AIDS). HTLV-III refers to prototype virus isolated from AIDS patients. Groups reported to be at greatest risk for AIDS include homosexual or bisexual males; intravenous drug users and Haitian immigrants to the United States. Hemophiliacs who receive blood products pooled from donors and recipients of multiple blood transfusions are also at risk. Clinical manifestations of AIDS include severe, unexplained immune deficiency which generally involves a depletion of helper T lymphocytes. These may be accompanied by malignancies and infections. The mortality rate for patients with AIDS is high. A less severe form of AIDS also exists, in which there may be lymphadenopathy and depressed helper T cell counts; there is not, however, the devastating illness characteristic of full-blown AIDS. There are many individuals, who are classified as having early AIDS (pre-AIDS), who exhibit these signs. It is not now possible to predict who among them will develop the more serious symptoms.

[0005] Much of the evidence implicates HTLV-III as the etiological agent of the infectious AIDS. First, there is consistent epidemiology; greater than 95% of the patients with AIDS have antibodies specific for HTLV-III. Second, there has been reproducible identification and isolation of virus in this disease; more than 100 variants of HTLV-III have been isolated from AIDS patients. Third, there has been transmission of the disease to normal healthy individuals who received blood transfusions from infected blood donors.

[0006] HTLV-III has been shown to share several properties with HTLV-I and HTLV-II but also to be morphologically, biologically and antigenically distinguishable. R. C. Gallo et al., Frequent Detection and Isolation of Cytopathic Retroviruses (HTLV-III) from Patients with AIDS and At Risk for AIDS. Science, 224:500-503. (1984). For example, HTLV-III has been shown to be antigenically related to HTLV-I and HTLV-II by demonstrating cross-reactivity with antibodies to HTLV-I and HTLV-II core proteins, p24 and p19, and envelope antigens and by nucleic acid cross-hybridization studies with cloned HTLV-I and HTLV-II DNAs. However, unlike HTLV-I and HTLV-II, it lacked the ability to infect and transform T cells from normal umbilical cord blood and bone marrow in vitro, and has the cytopathic effect on infected cells only.

[0007] Like the RNA genome of other retroviruses, the RNA genome of HTLV-III contains three genes which encode viral proteins: 1) the gag gene, which encodes the internal structural (nucleocapsid or core) proteins; 2) the pol gene, which encodes the RNA-directed DNA polymerase (reverse transcriptase); and 3) the env gene, which encodes the envelope glycoproteins of the virion. In addition, the HTLV-III genome contains a region designated Px, located between the env gene and the 3' LTR, which appears to be involved in functional killing of the virus.

[0008] At this time, AIDS is still difficult to diagnose before the onset of clinical manifestations. There is no method presently available for the prevention of the disease. Treatment of those with AIDS is generally not successful and victims succumb to the devastating effects HTLV-III has on the body.

SUMMARY OF THE INVENTION

[0009] This invention is based upon applicant's cloning of HTLV-III DNA in recombinant/vector host systems capable of expressing immunoreactive HTLV-III polypeptides. Based on the cloning of HTLV-III DNA in systems which express immunoreactive-polypeptides, applicant has developed methods useful in the diagnosis, treatment and prevention of AIDS. Applicant has developed methods of detecting HTLV-III and antibodies against HTLV-III in body fluids (e.g., blood, saliva, semen), and methods useful in immunotherapy (e.g., vaccination and passive immunization against AIDS). In addition, applicant has developed methods of making HTLV-III DNA probes and RNA probes useful in detecting HTLV-III in body fluids.

[0010] Polypeptides encoded by segments of the HTLV-III genome have been produced by these recombinant DNA methods. For example, polypeptides encoded by three regions of the HTLV-III genome (an env gene sequence, an env-lor gene sequence and a 1.1Kb EcoRI restriction fragment from HTLV-III cDNA) have been produced. The polypeptides expressed have been isolated. These polypeptides are immunoreactive with sera of patients having AIDS and with antibodies to HTLV-III and thus are useful in screening blood and other body fluids for the presence of antibodies against HTLV-III. Applicant's invention threfore provides a method not only for diagnosing AIDS, but also for preventing the transmission of the disease to others through blood or blood components harboring HTLV-III. The latter is particularly valuable in screening donated blood before it is transfused or used to obtain blood components (e.g., Factor VIII for the treatment of hemophilia; Factor IX)

[0011] Polypeptides produced by the recombinant DNA methods are employed in the production of antibodies, including monoclonal antibodies, against the virus. Such antibodies form the basis for immunoassay and diagnostic techniques for directly detecting HTLV-III in body fluids such as blood, saliva, semen, etc. Neutralizing antibodies against the virus may be used to passively immunize against the disease.

[0012] Applicant's cloning of HTLV-III DNA in such recombinant vector host systems also provides the basis for determination of the nucleotide sequence of HTLV-III DNA. The DNA probes are homologous to DNA regions which are unique to the HTLV-III genome. DNA probes provide another method of detecting HTLV-III in blood, saliva or other body fluids. RNA probes which contain regions unique to the HTLV-III genome can also be formed and used for the detection of HTLV-III in body fluids.

BRIEF DESCRIPTION OF THE FIGURES

[0013] FIG. 1 is a representation of HTLV-III DNA. FIG. 1a shows sites at which the genome is cut by the restriction enzyme SstI and FIG. 1b shows the fragments of HTLV-III genome produced through the action of restriction enzymes Kpn, EcoRI and Hind III.

[0014] FIG. 2 is a representation of HTLV-III DNA. FIG. 2a shows the location of restriction enzyme sites in the genome and FIG. 2b shows the location in the HTLV-III genome of DNA inserts in open reading frame clones. The (+) and (-) indicate reactivity and lack of reactivity, respectively, of the fusion protein expressed by cells transformed by the ORF vectors with sera of AIDS patients.

[0015] FIG. 3 shows the nucleotide sequence for HTLV-III DNA and the predicted amino acid sequence of the four longest open reading frames. Restriction enzyme sites are indicated above the nucleotide sequence.

[0016] FIG. 4 is an immunoblot showing the position on an SDS polyacrylamide gel of HTLV-III env-Beta-galactosidase fusion proteins.

[0017] FIG. 5 shows sites at which the genome is cut by the restriction enzyme EcoRI and construction of recombinant plasmids carrying HTLV-III DNA.

[0018] FIG. 6 is an immunoblot showing the positions on nitrocellulose blots of peptides produced by bacterial cells transformed by recombinant constructs ompA1-R-6; ompA2-R-7 and ompA3-R-3, into which a 1.1Kb EcoRI HTLV-III cDNA restriction fragment had been inserted. FIG. 6a shows the nucleotide sequence of the ompA signal peptide and the pertinent region of recombinant plasmids ompA1-R-6; ompA2-R-7 and ompA3-R-3.

[0019] FIG. 7 is an immunoblot showing blocking of reaction between HTLV-III antigens and an AIDS serum by lysates of E.coli containing HTLV-III DNA recombinant plasmid ompA1-R-6 (lanes 1-5) and no blocking of the reaction by lysates of E.coli control cells (lanes 6-10).

[0020] FIG. 8 is an immunoblot showing the presence or absence of antibodies against the peptide encoded by the 1.1Kb EcoRI HTLV-III restriction fragment of HTLV-III CDNA in sera from healthy individuals (lanes 1-3) and from AIDS patients (lanes 4-11). Purified HTLV-III virus (panel A) or total cell lysate of bacterial clone ompA1-R-6(OlR6) were reacted with sera samples.

[0021] FIG. 9 represents the open reading frame expression vector pMRIOO having HTLV-III DNA.

[0022] FIG. 10 represents lambdaCI-HTLV-III beta-galactosidase fusion proteins. FIG. 10a is an immunoblot showing the position on SDS polyacrylamide gel of lambdaCI-HTLV-III beta-galactosidase fusion proteins, and FIG. 10b shows the immunoreactivity of such proteins with sera from AIDS patients.

BEST MODE FOR CARRYING OUT THE INVENTION

[0023] Despite the similarity between HTLV-III and the other members of the HTLV-bovine leukemia virus (BLV) family of viruses, the biology and pathology of HTLV-III differs substantially. For example, relatively little homology has been found in the HTLV-III genome when compared with that of the HTLV-I or -II genome. Infection with HTLV-III often results in profound immunosuppression (AIDS), consequent to the depletion of the OKT4(+) cell population. This effect is mirrored by a pronounced cytopathic, rather than transforming, effect of HTLV-III infection upon the OKT4(+) cells in lymphocyte cultures in vitro. In contrast, infection with HTLV-I results in a low incidence of T-cell leukemia lymphoma (an OKT4(+) cell malignancy). There is evidence for some degree of immunodeficiency in HTLV-I patients as well. Infection of primary lymphocytes in culture by HTLV-I and -II results in vitro transformation of predominantly OKT4(+) cells. A cytopathic effect of HTLV-I infection upon lymphocytes is apparent, but the effect is not as pronounced as that observed for HTLV-III.

[0024] HTLV-III also differs from HTLV-I and -II in the extent of infectious virion production in vivo and in vitro. High titers of cell free, infectious virions can be obtained from AIDS patient semen and saliva and from the supernatant of cultures infected with HTLV-III. Very few, if any, cell free infectious virions can be recovered from adult T-cell leukemia lymphoma (ATLL) patients or from cultures infected with HTLV-I or -II.

[0025] Envelope glycoprotein is the major antigen recognized by the antiserum of AIDS patients. In this respect, HTLV resembles other retroviruses, for which the envelope glycoprotein is typically the most antigenic viral polypeptide. In addition, the neutralizing antibodies are generally directed toward the envelope glycoprotein of the retrovirus. Serum samples from 88 percent to 100 percent of those with AIDS have been shown to have antibodies reactive with antigens of HTLV-III; the major immune reactivity was directed against p41, the presumed envelope antigen of HTLV-III. Antibodies to core proteins have also been demonstrated in serum of AIDS patients, but do not appear to be as effective an indicator of infection as is the presence of antibodies to envelope antigen.

[0026] The p41 antigen of HTLV-III has been difficult to characterize because the viral envelope is partially destroyed during the process of virus inactivation and purification. This invention responds to the great need to characterize this antigenic component of the HTLV-III virus and to determine the existence and identity of other viral antigenic components in several ways. It provides products, such as HTLV-III polypeptides, antibodies to the polypeptides and RNA and DNA probes, as well as methods for their production. These serve as the basis for screening, diagnostic and therapeutic products and methods.

[0027] This invention relates to HTLV-III polypeptides which are produced by translation of recombinant DNA sequences encoding HTLV-III proteins. Polypeptides which are produced in this way and which are immunoreactive with serum from AIDS patients or antibodies to HTLV-III are referred to as recombinant DNA-produced immunoreactive HTLV-III polypeptides. They include, but are not limited to, antigenic HTLV-III core and envelope polypeptides which are produced by translation of the recombinant DNA sequences specific to the gag and the env DNA sequences encoding HTLV-III core proteins and envelope glycoproteins, respectively. They also include the polypeptides which are produced by translation of the recombinant DNA sequences included in a 1.1Kb EcoRI restriction fragment of HTLV-III cDNA and recombinant DNA sequences specific to the sor gene and the Px genes of HTLV-III. The sor DNA sequence is common to replication competent HTLV-III viruses. The Px genes contain a coding sequence with one large open reading frame (lor), located between the env gene and the 3' end of the HTLV-III genome. Both the env DNA sequences and the lor DNA sequences are located within the same open reading frame of the HTLV-III genome and this gene region is accordingly designated env-lor.

[0028] The polypeptides encoded by these regions of the HTLV III can be used in immunochemical assays for detecting antibodies against HTLV-III and HTLV-VIII infection. These methods can assist in diagnosing AIDS. In addition, they can also be employed to screen blood before it is used for transfusions or for the production of blood components (e.g., Factor VIII for the treatment of hemophilia). Availability of screening technics will reduce the risk of AIDS transmission.

[0029] Detection of antibodies reactive with the polypeptides can be carried out by a number of established methods. For example, an immunoreactive HTLV III polypeptide can be affixed to a solid phase (such as polystyrene bead or other solid support). The sold phase is then incubated with blood sample to be tested for antibody against HTLV-III. After an appropriate incubation period the solid phase and blood sample are separated. Antibody bound to the solid phase can be detected with labeled polypeptide or with a labeled antibody against human immunoglobulin.

[0030] HTLV-III polypeptides can be used in a vaccine prevention of AIDS. For vaccination against the virus, immunogenic polypeptides which elicit neutralizing antibody would be employed. The leading candidates for use in vaccines are the viral envelop polypeptides.

[0031] The polypeptides can also be used to produce antibodies, including monoclonal antibodies, against the HTLV-III polypeptides. These antibodies can be used in immunochemical assays for direct detection of the virus in body fluids (such as blood, saliva semen). Assays employing monoclonal antibody against specific HTLV III antigenic determinants will reduce false-positive results thereby improving accuracy of assays for the virus. Antibodies against the virus may also be useful in immunotherapy. For example, antibodies may be used to passively immunize against the virus.

[0032] The methods of producing the polypeptides are also a subject of this invention, as are diagnostic methods based on these polypeptides.

[0033] This invention also provides methods for the isolation of genes of HTLV-III which encode immunoreactive polypeptides; identification of the nucleotide sequence of these genes; introduction of DNA sequences specific to these viral DNA sequences into appropriate vectors to produce viral RNA and the formation of DNA probes. These probes are comprised of sequences specific to HTLV-III DNA and are useful, for example, for detecting complementary HTLV-III DNA sequences in body fluids (e.g., blood).

[0034] HTLV-III Polypeptides

[0035] Genetic engineering methods are used to isolate segments of HTLV-III DNA which encode immunoreactive HTLV-III polypeptides. Among these are polypeptides which are immunoreactive with serum from AIDS patients or antibodies to HTLV-III. These polypeptides include the core protein, a 15Kd peptide encoded by a 1.1Kb EcoRI HTLV-III restriction fragment of HTLV-III DNA and the envelope glycoprotein. These methods are also used to sequence the fragments which encode the polypeptides. The proviral genes integrated into host cell DNA are molecularly cloned and the nucleotide sequences of the cloned provirus is determined.

[0036] An E. coli expression library of HTLV-III DNA is constructed. The HTLV-III genome is cloned and cuts are then made in the cloned HTLV-III genome with restriction enzymes to produce DNA fragments. (FIGS. 1 and 2) HTLV-III DNA fragments of approximately 200-500bp are isolated from agarose gel, end repaired with T.sub.4 polymerase and ligated to linker DNA. The linker ligated DNA is then treated with a restriction enzyme, purified from agarose gel and cloned in an expression vector. Examples of the expression vectors used are: OmpA, pIN (A,B and C), lambda pL, T7, lac, Trp, ORF and lambda gt11. In addition, mammalian cell vectors such as pSV28pt, pSV2neo, pSVdhfr and VPV vectors, and yeast vectors, such as GALI and GAL10, may be used.

[0037] The bacterial vectors contain the lac coding sequences, into which HTLV-III DNA can be inserted for the generation of B-galactosidase fusion protein. The recombinant vectors are then introduced into bacteria (e.g., E.coli); those cells which take up a vector containing HTLV-III DNA are said to be transformed. The cells are then screened to identify cells which have been transformed and are expressing the fusion protein. For example, the bacteria are plated on MacConkey agar plates in order to verify the phenotype of clone. If functional B-galactosidase is being produced, the colony will appear red.

[0038] Bacterial colonies are also screened with HTLV-III DNA probes to identify clones containing the DNA regions of interest (e.g., HTLV-III a, pol and env DNA sequences). Clones which are positive when screened with the DNA probe and positive on the MacConkey agar plates are isolated.

[0039] This identification of cells harboring the HTLV-III DNA sequences makes it possible to produce HTLV-III polypeptides which are immunoreactive with HTLV-III specific antibody. The cells from the selected colonies are grown in culture under conditions allowing the expression of the hybrid protein. Cell protein is then obtained by means known in the art. For example, the culture can be centrifuged and the resulting cell pellet broken. Polypeptides secreted by the host cell can be obtained (without disruption of the cells) from the cell culture supernatant.

[0040] The total cellular protein is analysed by being run on an SDS polyacrylamide gel electrophoresis. The fusion proteins are identified at a position on the gel which contains no other protein. Western blot analyses are also carried out on the clones which screened positive. Such analyses are performed with serum from AIDS patients, with the result that it is possible to identify those clones expressing HTLV-III B-galactosidase fusion proteins (antigens) that cross-react with the HTLV-III specific antibody.

[0041] Lambda .sub.10 clones harboring HTLV-III DNA are cloned from the replicated form of the virus. As the retrovirus is replicating, double stranded DNA is being produced. The cloned HTLV-III DNA is digested with the restriction enzyme SstI. (FIG. 1a) Because there are two SstI recognition sites within the LTR of HTLV-III DNA, one LTR region is not present in the cloned DNA sequence removed from the lambda.sub.10 vector. As a result, a small (approximately 200 bp) fragment of the HTLV-III DNA is missing.

[0042] The resulting DNA is linearized and fragments are produced by digesting the linearized genomic DNA spanning the env gene region with restriction enzymes. For example, fragments are produced using Kpn or EcoRI plus HindIII, as shown in FIG. 1b. The resulting 2.3kb KpnI-KpnI fragments; 1.0kbEcoRI-EcoRI fragments and 2.4Kb EcoRI-HindIII fragments are isolated by gel electrophoresis and electro-elution. These fragments are randomly sheared to produce smaller fragments. The fragments thus produced are separatedfrom agarose gel and DNA fragments between about 200-500 bp are eluted.

[0043] The eluted 200-500bp DNA fragments are end filled through the use of E. coli T.sub.4 polymerase and blunt end ligated into an open reading frame expression (ORF) vector, such as pMR100. This ligation may occur at the SmaI site of the pMR100 vector, which contains two promoter regions, hybrid coding sequences of lambdaCI gene and lacI-LacZ gene fusion sequence. In the vector, these are out of frame sequences; as a result, the vector is nonproductive. The HTLV-III DNA is inserted into the vector; the correct DNA fragments will correct the reading frame, with the result that CI-HTLV-III-B-galactosidase fusion proteins are produced. The expression of the hybrid is under the control of the lac promoter. Based on the sequence of pMR100, it appears that if a DNA fragment insert cloned into the SmaI site is to generate a proper open reading frame between the lambdaCI gene fragment and the lac-Z fragment, the inserted DNAtmust not contain any stop codons in the reading frame set by the frame of the lambdaCI gene.

[0044] The recombinant pMIR100 vectors are then introduced into E. coli. The bacteria are plated on MacConkey agar plates to verify the phenotype of the clone. If functional B-galactosidase is being produced, the colony will appear red. The colonies are also screened with HTLV-III DNA probes, for the purpose of identifying those clones containing the insert. Clones which are positive when screened with the DNA probe and positive on the MacCohkey agar plates are isolated.

[0045] The cells from the selected colonies are grown in culture. The culture is spun down and the cell pellet broken. Total cellular protein is analysed by being run on an SDS polyacrylamide gel. The fusion proteins are identified at a position on the gel which contains no other protein. (FIG. 4) Western blot analyses are also carried out on the clones which screened positive. Sera from AIDS patients are used, thus making it possible to identify those clones which express the HTLV-III-B-galactosidase fusion proteins that cross-react with the HTLV-III specific antibody. 1000 clones were screened by this method; 6 were positive.

[0046] Because of the nature of the pMR100 cloning vehicle, a productive DNA insert should also be expressed as a part of a larger fusion polypeptide. HTLV-III env gene containing recombinant clones was identified by colony hybridization. The production of larger fusion polypeptides bearing functional B-galactosidase activity was verified by phenotype identification on MacConkey agar plates; by B-galactosidase enzymatic assays and by analysis on 75% SDS-polyacrylamide gels. Immunoreactivity of the larger protein with antibody to HTLV-III was assessed by western blot analysis using serum from AIDS patients. These large fusion proteins also reacted with anti-B-galactosidase and anti-CI antiserum. This finding is consistent with the hypothesis that they are proteins of CI-HTLV-III-lacIZ.

[0047] The open reading frame insert fragment of HTLV-III is further analyzed by DNA sequencing analysis. Because one of the two BamHI sites flanking the SmaI cloning site in pMR100 is destroyed in the cloning step, positive clones are digested with restriction enzymes HindIII and claI to liberate the inserted HTLV-III DNA fragment. The HTLV-III ORF inserts are isolated from the fusion recombinant and cloned into M13 sequencing cloning vector mp18 and mp19 digested with HindIII and AccI. DNA sequences of the positive ORF clones are then determined.

[0048] Fragments of HTLV-III DNA of approximately 200-500 bps are isolated from agarose gel, end repaired with T.sub.4 polymerase and ligated to EcoRI linker. The EcoRI linker ligated DNA is then treated with EcoRI purified from 1% agarose gel and cloned in an expression vector, lambda gt11. This vector contains lac Z gene coding sequences into which the foreign DNA can be inserted for the generation of B-galactosidase fusion protein. The expression of the hybrid gene is under the control of lac repressor. The lac repressor gene, lac I, is carried on a separate plasmid pMC9 in the host cell, E. coli Y1090. AIDS patient serum was used to probe the lambdagt11 library of HTLV-III genome DNA containing 1.5.times.10.sup.4 recombinant phage. In a screen of 5000 recombinants, 100 independent clones that produced strong signals were isolated. The positive recombinant DNA clones were further characterized for their specific gene expression. Rabbit hyperimmune serum against P24 was also used to identify the gag gene specific clones. Nick-translated DNA probes of specific HTLV-III gene, specifically the gag gene, env gene and Px gene were used to group the positive immunoreactive clones into specific gene region.

[0049] Recombinant clones that produced strong signals with AIDS serum and contain insert DNA spanning the HTLV-III ga, pol, sor and env-lor gene regions were examined in detail by mapping their insert with restriction enzymes and DNA sequencing analysis. Determination of the Nucleotide Sequence of HTLV-III DNA

[0050] Genetic engineering methods are used to determine the nucleotide sequence of HTLV-III DNA. One technique that can be used to determine the sequence is a shotgun/random sequencing methods. HTLV-III DNA is sheared randomly into fragments of about 300-500 bp in size. The fragments are cloned, for example, using m13, and the colonies screened to identify those having an HTLV-III DNA fragment insert. The nucleotide sequence is then generated, with multiple analysis producing overlaps in the sequence. Both strands of the HTLV-III DNA are sequenced to determine orientation. Restriction mapping is used to check the sequencing data generated.

[0051] The nucleotide sequence of one cloned HTLV-III genome (BH10) is shown in FIG. 3, in which the position of sequences encoding gag protein p17 and the N-terminus of gag p24 and the C-terminus of gag p15 (which overlaps with the N-terminus of the pol protein) are indicated. The open reading frames (ORF) for pol, sor and env-lor are also indicated. The sequence of the remaining 182 base pairs of the HTLV-III DNA not present in clone BH10 (including a portion of R, U5, the tRNA primer binding site and a portion of the leader sequence) was derived from clone HXB2. The sequences of two additional clones (BH8 and BH5) are also shown. Restriction enzyme sites are listed above the nucleotide sequence; sites present in clone BH8 but not in clone BH10 are in parentheses. Deletions are noted ([]) at nucleotides 251, 254, 5671 and 6987-7001. The nucleotide positions (to the right of each line) start with the transcriptional initiation site. The amino acid residues are numbered (to the right of each line) for the four largest open reading frames starting after the preceding termination codon in each case except gag which is enumerated from the first methionine codon. A proposed peptide cleavage site (V) and possible asparagine-linked glycosylation sites are shown (*) for the env-lor open reading frame. The sequences in the LTR derived from clones BH8 and BH10 listed in the beginning of the figure are derived from the 3'-portion of each clone and are assumed to be identical to those present in the 5'-LTR of the integrated copies of these viral genomes.

[0052] Clone HXB2 was derived from a recombinant phage library of XbaI digested DNA from HTLV-III infected H9 cells cloned in lambdaJ1. H9 cells are human leukemic cells infected by a pool of HTLV-III from blood of AIDS patients, F. Wong-Staal, Nature, 312, November, 1984. Cloning vector clones BH10, BH8, and BH5 were derived from a library of SstI digested DNA from the Hirt supernatant fraction of HTLV-III infected H9 cells cloned in lambdagtWes.lambdaB. Both libraries were screened with cDNA probe synthesized from virion RNA using oligo.dT as a primer. Clones BH8, BH5, and a portion of HXB2 were sequenced as described by Maxam and Gilbert. (1980) Maxam, A. M. and Gilbert, Co. Methods in Enzymology. 65: 499-560. Clone BH10 was sequenced by the method of Sanger modified by the use of oligonucleotides complementary to the M13 insert sequence as primers and using Klenow fragment of DNA polymerase I or reverse transcriptase as the polymerase.

[0053] Formation of RNA, RNA Probes and DNA Probes Specific to HTLV-III

[0054] DNA sequences which are an entire gene or segment of a gene from HTLV-III are inserted into a vector, such as a T7 vector. In this embodiment, the vector has the Tceu promoter from the T cell gene 10 promoter and DNA sequences encoding eleven amino acids from the T cell gene 10 protein.

[0055] The vectors are then used to-transform cells, such as E. coli. The T7 vector makes use of the T7 polymerase, which catalyzes RNA formation and recognizes only T7 promoter, which is the site where RNA polymerase binds for the initiation of transcription. The T7 polymerase does not recognize E. coli promoter. As a result, if HTLV-III DNA sequences are inserted after the promoter and polymerase genes of the T7 vector, which recognizes them to the exclusion of other signals, and a terminator is placed immediately after the HTLV-III DNA sequences, the T7 vector will direct manufacture RNA complementary to the HTLV-III DNA insert.

[0056] Determination of the nucleotide sequence of HTLV-III DNA also provides the basis for the formation of DNA probes. Both RNA proves and DNA HTLV-III probes must have a distinctive region of the HTLV-III genome in order to be useful in detecting HTLV-III in body fluids. There is relatively little homology between the HTLV-III genome and the HTLV-I and -II genomes and probes contain regions which are unique to HTLV-III (i.e., not shared with HTLV-I or -II). For example, nucleotide sequences in the env gene region of HTLV-III can be used.

[0057] Either viral RNA or DNA can be used for detecting HTLV-III in, for example, saliva, which is known to have a very high concentration of the virus. This can be done, for example, by means of a dot blot, in which the saliva sample is denatured, blotted onto paper and then screened using either type of probe. If saliva is used as the test fluid, detection of HTLV-III is considerable faster and easier than is the case if blood is tested.

[0058] Production of Monoclonal Antibodies Reactive with HTLV-III Polypeptides

[0059] Monoclonal antibodies reactive with HTLV-III polypeptides are produced by antibody-producing cell lines. The antibody-producing cell lines may be hybridoma cell lines commonly known as hybridomas. The hybrid cells are formed by fusion of cells which produce antibodv to HTLV-III polypeptide and an immortalizing cell, that is, a cell which imparts long term tissue culture stability on the hybrid cell. In the formation of the hybrid cell lines, the first fusion partner--the antibody-producing cell--can be a spleen cell of an animal immunized against HTLV-III polypeptide. Alternatively, the antibody-producing cell can be isolated B lymphocyte which produces antibody against an HTLV-III antigen. The lymphocyte can be obtained from the spleen, peripheral blood, lymph nodes or other tissue. The second fusion partner--the immortal cell--can be a lymphoblastoid cell or a plasmacytoma cell such as a myeloma cell, itself an antibody-producing cell but also malignant.

[0060] Murine hybridomas which produce monoclonal antibodies against HTLV-III polypeptide are formed by the fusion of mouse myeloma cells and spleen cells from mice immunized against the polypeptide. To immunize the mice, a variety of different immunization protocols may be followed. For instance mice may receive primary and boosting immunizations of the purified polypeptide. The fusions are accomplished by standard procedures. Kohler and Milstein, (1975) Nature (London) 256, 495-497; Kennet, R., (1980) in Monoclonal Antibodies (Kennet et al., Eds. pp. 365-367, Plenum Press, NY).

[0061] The hybridomas are then screened for production of antibody reactive with the polypeptide. This can be performed by screening procedures known in the art.

[0062] Another way of forming the antibody-producing cell line is by transformation of antibody-producing cells. For example, a B lymphocyte obtained from an animal immunized against HTLV-III polypeptide may be infected and transformeed with a virus such as the Epstein-Barr virus in the case of human B lymphocytes to give an immortal antibody-producing cell. See, e.g., Kozbor and Rodor (1983) Immunology Today 4(3), 72-79. Alternatively, the B lymphocyte may be transformed by a transforming gene or transforming gene product.

[0063] The monoclonal antibodies against HTLV-III polypeptide can be produced in large quantities by injecting antibody-producing hybridomas into the peritoneal cavity of mice and, after an appropriate time, harvesting the ascites fluid which contains very high titer of homogenous antibody and isolating the monoclonal antibodies therefrom. Xenogeneic hybridomas should be injected into irradiated or athymic nude mice. Alternatively, the antibodies may be produced by culturing cells which produce HTLV-III polypeptide in vitro and isolating secreted monoclonal antibodies from the cell culture medium. The antibodies produced according to these methods can be used in diagnostic assays (e.g., detecting HTLV-III in body fluids) and in passive immunotherapy. The antibodies reactive with HTLV-III polypeptides provide the basis for diagnostic tests for the detection of AIDS or the presence of HTLV-III in biological fluids (e.g., blood, semen, saliva) and for passive immunotherapy. For example, it is possible to produce anti p 41, to attach it to a solid phase using conventional techniques and to contact the body fluid to be tested with the immobilized antibody. In this way, HTLV-III (antigen) can be detected in the body fluid; this method results in far fewer false positive test results than do tests, in which antibody against HTLV-VIII is detected.

[0064] This invention will now be further illustrated by the following examples.

EXAMPLE 1

[0065] Preparation of Sonicated DNA Fragments

[0066] 10 ug of gel purified HTLV-III restriction fragments were sonicated to fragment size on average of 500 bps. After sonication, the DNA was passed through a DEAE-cellulose column in 0.1.times.TBE in order to reduce the volume. The DEAE-bound DNA was washed with 5 ml of 0.2 M NaCl-TE (2 M NaCl, 10 mm Tris HCl pH 7.5, 1 mM EDTA) and then eluted with 1 M NaCl-TE, and ethanol precipitated. The size range of the sonicated DNA was then determined on 1.2% agarose gel. DNA fragments of desired length (200-500 bps) was eluted from the gel. T4 DNA polymerase was used to fill in and/or trim the single strand DNA termini generated by the sonication procedure. DNA fragments were incubated with T4 polymerase in the absence of added nucleotides for five minutes at 37.degree. C. to remove nucleotides from 3' end and then all 4 nucleotide precursors were added to a final concentration of 100 uM and the reaction mixture was incubated another 30 minutes to repair the 5'-end single stranded overhang. The reaction was stopped by heat inactivation of the enzyme at 68.degree. C. for 10 minutes. DNA was phenol extracted once, ethanol precipitated and resuspended in TE.

EXAMPLE 2

[0067] Cloning of Random Sheared DNA Fragments

[0068] The sonicated blunt end repaired HTLV-III DNA fragments were ligated into the SmaI site of the ORF expression vector pMR100 and transformed into host cell LG90 using standard transformation procedures. B-galactosidase positive phenotype of the transformant were identified by plating the transformed cell on ampicillin (25 ug/ml) containing McConkey agar plates and scoring the phenotype after 20 hours at 37.degree. C.

EXAMPLE 3

[0069] Hybrid Protein Analysis

[0070] Ten milliliter samples of cells from an overnight saturated culture grown in L broth containing ampicillin (25 ug/ml) were centrifuged, the cell pellet was resuspended in 500 ul of 1.2 fold concentrated Laemmli sample buffer. The cells were resuspended by vortexing and boiling for 3 minutes at 100.degree. C. The lysate was then repeated by being forced through a 22 guage needle to reduce the lysate viscosity. Approximately 10 ul of the protein samples were electrophoresed in 7.5% SDS-PAGE (SDS-polyacrylamide) gels.

[0071] Electrophoretic transfer of proteins from SDS-PAGE gels to nitrocellulose paper was carried out according to Towbin et. al.. After the transfer, the filter was incubated at 37.degree. C. for two hours in a solution of 5% (w/v) nonfat milk in PBS containing 0.1% antifoam A and 0.0001% merthiolate to saturate all available protein binding sites. Reactions with AIDS antisera were carried out in the same milk buffer containing 1% AIDS patient antisera that had been preabsorbed with E. coli lysate. Reactions were performed in a sealed plastic bag at 4.degree. C. for 18-24 hours on a rotatory shaker. Following this incubation, the filter was washed three times for 20 minutes each at room temperature in a solution containing 0.5% deoxycholic, 0.1 M NaCl, 0.5% triton X-100, 10 mm phosphate buffer pH 7.5 and 0.1 mM PMSF.

[0072] To visualize antigen-antibody interactions, the nitrocellulose was then incubated with the second goat antihuman antibody that had been iodinated with .sup.125I. The reaction with the iodinated antibody was carried out at room temperature for 30 minutes in the same milk buffer as was used for the first antibody. The nitrocellulose was then washed as previously described and exposed at -70.degree. C. using Kodak XAR5 film with an intensifying screen.

EXAMPLE 4

[0073] Screening of the HTLV-III ORF Library by Colony Hybridization

[0074] E. coli LG90 transformants were screened with HTLV-III DNA probes containing the DNA regions of interest (e.g. HTLV-III gag, env or Px gene specific sequences). Colonies were grown on nitrocellulose filter and screened according to the procedure of Grunstein and Hogness by using a nick-translated HTLV-III DNA as hybridization probe.

[0075] The DNA fragment was in general excised by restriction endonuclease digestion, gel purified, and .sup.32P-labeled to a specific activity of 0.5.times.10.sup.8 cpm/ug by nick-translation (Rigby, P. W. J. et al., J. Mol. Biol. 113, 237 (1977). Duplicate nitrocellulose filters with DNA fixed to them were prehybridized with 6.times.SSC (0.9 Ml NaCl/0.09 M sodium citrate, pH 7.0), 5.times. Denhardt's solution (Denhardt's solution: 0.02% each of polyvinylpyrrolidone, Ficoll and bovine serum albumin) 10 ug of denatured sonicated E. coli DNA per ml at 55.degree. C. for 3-5 hours. The filters were then placed in a fresh sample of the same solution to which the denatured hybridization probe had been added. Hybridization was permitted to take place at 68.degree. C. for 16 hours. The filters were washed repeatedly in 0.3.times.SSC at 55.degree. C., and then exposed to x-ray film.

EXAMPLE 5

[0076] Recombinant DNA Produced Peptide of HTLV-III which is Immunoreactive with Sera From Patients with AIDS

[0077] An expression vector, pIN-III-ompA (ompA) was used. ompA has the lipoprotein (the most abundant protein in E.coli) gene promoter (lpp) and the lacUV5 promoter-operator (FIG. 1). ompA vectors also contain the DNA segment encoding the lac repressor, which allows the expression of the inserted DNA to be regulated by lac operon inducers such as IPTG. The ompA cloning vehicles contain three unique restriction enzyme sites EcoRI, HindIII, Bam HI in all three reading frames and permit the insertion of DNA into any of these restriction sites.

[0078] Various restriction fragments were excised from the recombinant clone, lambdaBH10, which contains a 9 Kb long HTLV-III DNA insert in the SstI site of the vector lambdagtWES lambdaB. These restriction fragments were them inserted into the ompA vectors at all three reading frames and used to transform E.coli JA221 cells. Transformants were first screened for HTLV-III DNA by in situ colony hybridization using nick-translated HTLV-III DNA probes. The positive clones were then screened for expression of HTLV-III antigenic peptides using HTLV-III specific antibodies. For this, lysates of E.coli cell containing HTLV-III DNA recombinant plasmids were electrophoresed on 12.5% SDS-polyacrylamide gel and electroblotted onto nitrocellulose filters. The filters were then incubated first with well-characterized sera from AIDS patients and next with .sup.125I-labelled goat anti-human IgG antibodies. The washed filters were autoradiographed to identify peptides reactive with anti-HTLV-III antibodies.

[0079] Several gene segments that encode peptides showing immunoreactivity with anti-HTLV-III antibodies were demonstrated. Among these is a 1.1 Kb EcoRI restriction fragment. This fragment was inserted into ompA vectors in all three reading frames (FIG. 5). Cells were grown at 37.degree. C. in L broth containing 100 mg/ml. ampicillin to an OD.sub.600 of 0.2. At this time, the cell cultures were divided into two aliquots. IPTG was added to one aliquot to a final concentration of 2 mM (induced). IPTG was not added to the other aliquot (uninduced). Upon IPTG induction, transformants of all three plasmid constructs (designated OmpA.sub.1-R-6 (O1R6), OmpA 2-R-7 (O2R7), and OmpA.sub.3-R-3 (O3R3)) produced a 15 Kd peptide that is strongly reactive with anti-HTLV-III antibodies in sera from AIDS patients (FIG. 6 lane 1, purified HTLV-III virions; lanes 2 and 3, O1R6 uninduced and induced; lanes 4 and 5, O2R7 uninduced and induced; lanes 6 and 7 O3R3 uninduced and induced). This reactivity is not detected when sera from normal individuals is used.

[0080] DNA sequence data of the HTLV-III genome indicates that there is an open reading frame inside the pol gene located at the 5'-end of the EcoRI fragment. DNA sequence analysis of the three recombinant constructs, O1R6, O2R7 and P3R3, confirmed that each of these recombinants has a different reading frame of the HTLV-III plus strand coupled to the coding sequence of each vector. Only in O3R3 is the reading frame of the inserted DNA in phase with that set by the signal peptide in the ompA vector; in O1R6 and O2R7 the pol gene segment DNA is out of phase (FIG. 6a).

[0081] There is a 6 bp ribosome binding site, AAGGAG (Shine-Dalgarno sequence), located at nucleotide position 24-29 and an initiation codon, ATG, located 11 bp downstream (position 41-43). The 15 Kd peptide synthesized by all three recombinants appears to be translated from the transcripts using this internal initiation codon. If this is true, the peptide starts from the ATG located at position 41-43 and ends at the stop codon at position 446-448, producing a peptide of 135 amino acid residues encoded by the 3'-end segment of the pol gene of HTLV-III.

[0082] In addition to the 15 Kd peptide, the O3R3 construct, in which the reading frame of the HTLV-III DNA pol gene is in phase with that set by the vector, produced two additional peptides about 19 Kd and 16.5 Kd in size (FIG. 6). It is possible that the 19 Kd peptide contains an additional 35 amino acid residues, 21 of which are from the signal peptide encoded by the ompA.sub.3 vector and 14 encoded by the inserted HTLV-III DNA itself. The 16.5 Kd peptide may be the processed 19 Kd peptide in which the signal peptide is cleaved.

[0083] The O1R6 and O2R7 constructs also produces another peptide of about 17.5 Kd (FIG. 6) and weakly reactive with sera of AIDS patients. The origin of this peptide is not clear. The 1.1 Kb EcoRI fragment contains a second potential coding region designated as the short open reading frame (SOR) extending from nucleotide position 360 to 965 (FIG. 5). Four of the five AUG methionine codons in this region are near the 5'-end of this open reading frame. This DNA segment could encode peptides of 192, 185, 177 or 164 amino acid residues. However, there is no clearly recognizable ribosome binding site at the 5'-end of this open reading frame.

[0084] Further evidence also supports the conclusion that the 15 Kd peptide is indeed derived from the pol gene. First, deletion of the 3'-end StuI to EcoRI fragment from the 1.1 Kb EcoRI insert from O1R6, O2R7 and O3R8 (FIG. 5) does not affect the synthesis of the 15 Kd peptide. Second, clones containing only the 5'-end EcoRI to NdeI fragment still produce the same 15 Kd peptide. Finally, several recombinant clones containing various DNA fragments having the SOR coding sequence properly inserted into the open reading frame cloning vector, pMR100, produced lambdaCI-HTLV-III B-galactosidase tripartite fusion proteins which have very little immunoreactivity with anti-HTLV-III antibodies present in sera from AIDS patients.

[0085] Significant immunoreactivity against the 15 Kd peptide derived from the viral pol gene in sera from AIDS patients was detected. The identity of this immunoreactive peptide, with respect to the banding pattern of HTLV-III virion antigen in SDS-polyacrylamide gel electrophoresis, was determined by means of a competition inhibition inmunoassay. Purified HTLV-III virions were treated with SDS, electrophoresed, and electroblotted onto a nitrocellulose filter. Identical filter strips containing disrupted HTLV-III virions were incubated with well characterized serum from an AIDS patient in the presence or absence of lysates of O1R6, 02R7, or control bacterial clones. The specific immunoreaction between anti-HTLV-III antibodies present in sera of the AIDS patients and the blotted virion proteins were then revealed by .sup.125I-labeled goat anti-human antibody. As shown in FIG. 7, lysates of O1R6 block the immunoreactivity of the viral p31 protein with the AIDS serum, while lysates of control cells do not. This result suggests that the recombinant 15 Kd peptide encoded by 3'-end of the-viral pol gene is also a part of another virion protein, p31, in contrast to the view shared by some that p31 is a cellular protein which co-purifies with HTLV-III virions.

[0086] The prevalence in the sera of AIDS patients of antibodies against the 15 Kd peptide was also evaluated. In Western blot analysis employing the lysate of O1R6 as the source of antigen, a panel of coded sera from AIDS patients and normal healthy individuals was tested. All of the 20 AIDS sera and none of the 8 normal controls reacted with the 15 Kd peptide. Representative results are shown in (FIG. 8). These data indicate that most, if not all, AIDS patients produce antibodies against the viral p31 protein.

EXAMPLE 6

[0087] Expression in E. coli of Open Reading Frame Gene Segments of HTLV-III

[0088] HTLV-III DNA-was excised from lambda BH-10, which is a previously constructed recombinant lambda phage containing a 9 Kb segment of HTLV-III DNA inserted into the vector lambdagtwes lambda B (FIG. 2a). This HTLV-III DNA was sonicated and DNA fragments of about 0.5 Kb purified by gel electrophoresis, end repaired,- and inserted into the SmaI site of the open reading frame (ORF) vector, pMR100 (FIG. 9). This vector contains a bacterial lac promotor DNA segment linked to a second DNA fragment containing a hybrid coding sequence in which the N-terminus (5' segment) of the lambda CI gene of bacteriophage lambda is fused to an N-terminal-deleted lacIZ gene (3' segment). A short linker DNA fragment, containing a SmaI cloning site, has been inserted between these two fragments in such a manner that a frame shift mutation has been introduced upstream of the lacIZ-coding DNA. As a result, pMR100 does not produce any detectable B-galactosidase activity when introduced into cells of the Lac host E. coli LG90. The insertion of foreign DNA containing an open reading frame, in this case the HTLV-III DNA, at the SmaI cloning site can reverse the frame shift mutation if the inserted coding sequence is in the correct reading frame with respect to both the lambdaCI leader and the lacIZ gene. Transformants were screened on MacConkey plates to detect individual clones that expressed B-galactosidase enzymatic activity in situ.

[0089] Among the 6000 ampicillin resistant transformants screened, about 300 were found to express B-galactosidase activity. Colony hybridization using .sup.32p-labelled nick-translated HTLV-III DNA as a probe revealed that all these Lac.sup.+ clones contained HTLV-III DNA. In the Lac.sup.+ clones the HTLV-III fragment inserted into the Sma I site of pMR100 must contain no stop codons in the reading frame set by the lambdaCI leader segment and the lacIZ gene must also be in the correct translational reading frame. The three-element-fused genes were expressed as tripartite fusion proteins, having a portion of the lambdaCI protein at the N-terminus, the HTLV-III segment in the middle, and the lacIZ polypeptide at the C-terminus.

[0090] The proteins produced by the Lac clones were analyzed by resolving cell lysates on 7.5% SDS-polyacrylamide gels along with those of the control Lac.sup.+ clone pMR200, which produced a lambdaCI-B-galactosidase fusion protein. The lacIZ gene in pkIR200 is identical to that in pMR100 except that it has a single base pair deletion which brings it in phase with the lambdaCI gene to produce an active B-galactosidase. By virtue of the very large size of the B-galactosidase and its fusion protecins, they are separated from the bulk of proteins in the cell lysates on the SDS-polyacrylamide gels and can be easily identified by Coomassie brilliant blue staining as shown in FIG. 10a. Some of the Lac.sup.+ clones containing HTLV-III DNA produce polypeptides that are larger (15,000 to 27,000 daltons) than the lambdaCI-lacIZ fusion protein. These findings are consistent with data that the DNA inserts are up to 700 bp long. The B-galactosidase fusion proteins accounted for about 1-2% of total cellular protein.

[0091] The peptides produced by the Lac.sup.+ clones were examined by Western blot analysis for immunoreactivity with sera from AIDS patients. After the lysates of Lac clones were electrophoresed in SDS-polyacrylamide gels, they were electro-transferred to nitrocellulose filters. These protein blots were first reacted with AIDS patient sera and then with .sup.125I-labeled goat anti-human IgG. The autoradiograph in FIG. 10b shows the immunoreactivity of a representative fused protein with the serum from an AIDS patient. The recombinant peptides also reacted with anti-B-galactosidase antiserum, consistent with the proposition that they had the general structure lambdaCI-HTLV-III peptide-LacIZ. Prom the immunoreactivity pattern of the negative controls, pMR100 and pMR200, which do not contain an HTLV-III DNA insert, it is evident that this particular AIDS serum contains antibodies reactive with several bacterial proteins of the host E. coli. This is not surprising, since AIDS patients are usually infected with a number of bacteria. Absorbing AIDS patient sera with Sepharose 4B conjugated with E. coli extract reduced the background immunoreactivity to some extent but did not completely eliminate it.

[0092] About 300 independent HTLV-III DNA-containing Lac colonies were analyzed in SDS polyacrylamide gels using Coomassie brilliant blue staining and Western blotting. About half of them were found to express fusion proteins containing extra peptides of about 100-200 amino acids, corresponding to DNA inserts of 300-600 bp long. Of these fusion proteins, 20 were found to react specifically with sera from AIDS patients. The unreactive clones probably contain peptides that fold in such a way that they are not reactive with antibodies or correspond to regions of HTLV-III protein molecules which are not immunogenic in AIDS patients. The other half of the Lac clones expressed fusion proteins whose sizes were not obviously different from that of the lambdaCI B-galactosidase protein. None from this group of fusion proteins was found to react with sera from AIDS patients.

[0093] The HTLV-III DNA inserts from Lac ORF clones were mapped to specific segments in the HTLV-III genome using Southern blotting procedures. In these studies, each plasmid clone was labelled with .sup.32P by nick-translation and hybridized to a battery of HTLV-III DNA restriction fragments. This hybridization analysis mapped all of the Lac ORF clones into four open reading frame segments designated ORF-A, ORF-B, ORF-C, and ORF-D (FIG. 2a) consistent with the DNA sequencing data. The open reading frames ORF-A and -B, corresponding to the coding regions of the gag and pol genes, are 1.5 Kb and 3.0 Kb long, respectively. ORF-C is about 0.6 Kb long, slightly overlaps with the ORF-B region, and is capable of encoding a polypeptide of 21 overlaps with the ORF-B region, and is capable of encoding a polypeptide of 21 Kd. The location of ORF-C and its overlap with the pol gene are reminiscent of the structure of the env genes in HTLV-I and -II. However, ORF-C, designated as the short open reading frame (sor), is too short to code for the entire envelope protein. The fourth open reading frame, ORF-D, is 2.5 Kb long and could encode both a large precursor of the major envelope glycoprotein and another protein derived from the 39 terminus, which may be analogous to the lor products of HTLV-I and -II. This gene region of HTLV-III, designated env-lor, is at least twice as long as the lor of HTLV-I and HTLV-II and it is presently unclear whether single or multiple proteins are encoded herein.

[0094] Both Southern blotting and DNA sequencing studies were employed to analyze a number of clones. As shown in FIG. 2b, the Lac.sup.+ ORF clones expressing fusion proteins immunoreactive with sera from AIDS patients were located in ORF-A (e.g. #175 and 4191), ORF-B (e.g. #13, 31, and 162), or ORF-D (e.g. #113, 121, and 127) and not in the sor region. Not all peptides in these regions were immunoreactive, e.g. ORF clone #76 located in ORF-D.

[0095] Analysis of the open reading frame structures in HTLV-III posed questions as to which open reading frame(s) corresponds to the env gene. It is possible that the env-lor region in HTLV-III contains all or a part of the env gene in addition to the presumed lor gene. Recent evidence suggests that the lor in HTLV-I encodes a 42 Kd protein involved in the process of viral activation and transformation. When the lysate of one of the ORF clones (#127 in FIG. 2b) was tested against sera from 20 AIDS patients and 12 healthy normals in a strip radioimmunoassay based on the Western blot technique, immunoreactivity against the lambdaCI-HTLV-III-B-galactasidase fusion polypeptide was detected in the sera from 19 of the AIDS patients and none from normal controls. This result indicates that the protein encoded by the portion of the env-lor region contained in ORF clone #127 is produced in HTLV-III infected cells and induces antibody production in most if not all AIDS patients.

[0096] Industrial Applicability

[0097] This invention has industrial applicability in screening for the presence of HTLV-III DNA in body fluids and the diagnosis of AIDS.

[0098] Equivalents

[0099] Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific substantces and procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the following claims.

Sequence CWU 1

1

11 1 492 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(492) standard_name= "Clone BH10" / note = "Corresponds to nucleotide positions -453 to 39 in figure 3 of US 06/693,866" 1 tggaagggct aattcactcc caacgaagac aagatatcct tgatctgtgg atctaccaca 60 cacaaggcta cttccctgat tagcagaact acacaccagg gccagggatc agatatccac 120 tgacctttgg atggtgctac aagctagtac cagttgagcc agagaagtta gaagaagcca 180 acaaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatggaatg gatgacccgg 240 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac atggcccgag 300 agctgcatcc ggagtacttc aagaactgct gacatcgagc ttgctacaag ggactttccg 360 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat 420 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga 480 gcctgggagc tc 492 2 492 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(492) /standard_name= "Clone BH8" /note= "Corresponds to nucleotide positions -453 to 39 in figure 3 of US 06/693,866" 2 tggaagggct aattcactcc caacgaagac aagatatcct tgatctgtgg atccaccaca 60 cacaaggcta cttccctgat tggcagaact acacaccagg gccaggagtc agatatccac 120 tgacctttgg atggtgctac aagctagtac cagttgagcc agagaagtaa gaagaagcca 180 ataaaggaga gaacaccagc ttgttacacc ctgtgagcct gcatggaatg gatgaccctg 240 agagagaagt gttagagtgg aggtttgaca gccgcctagc atttcatcac atggcccgag 300 agctgcatcc ggagtacttc aagaactgct gatatcgagc ttgctacaag ggactttccg 360 ctggggactt tccagggagg cgtggcctgg gcgggactgg ggagtggcga gccctcagat 420 cctgcatata agcagctgct ttttgcctgt actgggtctc tctggttaga ccagatctga 480 gcctgggagc tc 492 3 182 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(182) /standard_name= "Clone HXB2" /note= "Corresponds to nucleotide positions 40 to 221 in figure 3 of US 06/693,866" 3 tctggctaac tagggaaccc actgcttaag cctcaataaa gcttgccttg agtgcttcaa 60 gtagtgtgtg cccgtctgtt gtgtgactct ggtaactaga gatccctcag acccttttag 120 tcagtgtgga aaatctctag cagtggcgcc cgaacaggga cctgaaagcg aaagggaaac 180 ca 182 4 8933 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(8933) /standard_name= "Clone BH10" /note= "Corresponds to nucleotide positions 222 to 9154 in figure 3 of EP 85307260" 4 gagctctctc gacgcaggac tcggcttgct gaagcgcgca cggcaagagg cgaggggcgg 60 cgactggtga gtacgccaaa aattttgact agcggaggct agaaggagag agatgggtgc 120 gagagcgtca gtattaagcg ggggagaatt agatcgatgg gaaaaaattc ggttaaggcc 180 agggggaaag aaaaaatata aattaaaaca tatagtatgg gcaagcaggg agctagaacg 240 attcgcagtt aatcctggcc tgttagaaac atcagaaggc tgtagacaaa tactgggaca 300 gctacaacca tcccttcaga caggatcaga agaacttaga tcattatata atacagtagc 360 aaccctctat tgtgtgcatc aaaggataga gataaaagac accaaggaag ctttagacaa 420 gatagaggaa gagcaaaaca aaagtaagaa aaaagcacag caagcagcag ctgacacagg 480 acacagcagt caggtcagcc aaaattaccc tatagtgcag aacatccagg ggcaaatggt 540 acatcaggcc atatcaccta gaactttaaa tgcatgggta aaagtagtag aagagaaggc 600 tttcagccca gaagtaatac ccatgttttc agcattatca gaaggagcca ccccacaaga 660 tttaaacacc atgctaaaca cagtgggggg acatcaagca gccatgcaaa tgttaaaaga 720 gaccatcaat gaggaagctg cagaatggga tagagtacat ccagtgcatg cagggcctat 780 tgcaccaggc cagatgagag aaccaagggg aagtgacata gcaggaacta ctagtaccct 840 tcaggaacaa ataggatgga tgacaaataa tccacctatc ccagtaggag aaatttataa 900 aagatggata atcctgggat taaataaaat agtaagaatg tatagcccta ccagcattct 960 ggacataaga caaggaccaa aagaaccttt tagagactat gtagaccggt tctataaaac 1020 tctaagagcc gagcaagctt cacaggaggt aaaaaattgg atgacagaaa ccttgttggt 1080 ccaaaatgcg aacccagatt gtaagactat tttaaaagca ttgggaccag cggctacact 1140 agaagaaatg atgacagcat gtcagggagt aggaggaccc ggccataagg caagagtttt 1200 ggctgaagca atgagccaag taacaaatac agctaccata atgatgcaga gaggcaattt 1260 taggaaccaa agaaagatgg ttaagtgttt caattgtggc aaagaagggc acacagccag 1320 aaattgcagg gcccctagga aaaagggctg ttggaaatgt ggaaaggaag gacaccaaat 1380 gaaagattgt actgagagac aggctaattt tttagggaag atctggcctt cctacaaggg 1440 aaggccaggg aattttcttc agagcagacc agagccaaca gccccaccat ttcttcagag 1500 cagaccagag ccaacagccc caccagaaga gagcttcagg tctggggtag agacaacaac 1560 tccccctcag aagcaggagc cgatagacaa ggaactgtat cctttaactt ccctcagatc 1620 actctttggc aacgacccct cgtcacaata aagatagggg ggcaactaaa ggaagctcta 1680 ttagatacag gagcagatga tacagtatta gaagaaatga gtttgccagg aagatggaaa 1740 ccaaaaatga tagggggaat tggaggtttt atcaaagtaa gacagtatga tcagatactc 1800 atagaaatct gtggacataa agctataggt acagtattag taggacctac acctgtcaac 1860 ataattggaa gaaatctgtt gactcagatt ggttgcactt taaattttcc cattagccct 1920 attgagactg taccagtaaa attaaagcca ggaatggatg gcccaaaagt taaacaatgg 1980 ccattgacag aagaaaaaat aaaagcatta gtagaaattt gtacagaaat ggaaaaggaa 2040 gggaaaattt caaaaattgg gcctgagaat ccatacaata ctccagtatt tgccataaag 2100 aaaaaagaca gtactaaatg gagaaaatta gtagatttca gagaacttaa taagagaact 2160 caagacttct gggaagttca attaggaata ccacatcccg cagggttaaa aaagaaaaaa 2220 tcagtaacag tactggatgt gggtgatgca tatttttcag ttcccttaga tgaagacttc 2280 aggaagtata ctgcatttac catacctagt ataaacaatg agacaccagg gattagatat 2340 cagtacaatg tgcttccaca gggatggaaa ggatcaccag caatattcca aagtagcatg 2400 acaaaaatct tagagccttt taaaaaacaa aatccagaca tagttatcta tcaatacatg 2460 gatgatttgt atgtaggatc tgacttagaa atagggcagc atagaacaaa aatagaggag 2520 ctgagacaac atctgttgag gtggggactt accacaccag acaaaaaaca tcagaaagaa 2580 cctccattcc tttggatggg ttatgaactc catcctgata aatggacagt acagcctata 2640 gtgctgccag aaaaagacag ctggactgtc aatgacatac agaagttagt ggggaaattg 2700 aattgggcaa gtcagattta cccagggatt aaagtaaggc aattatgtaa actccttaga 2760 ggaaccaaag cactaacaga agtaatacca ctaacagaag aagcagagct agaactggca 2820 gaaaacagag agattctaaa agaaccagta catggagtgt attatgaccc atcaaaagac 2880 ttaatagcag aaatacagaa gcaggggcaa ggccaatgga catatcaaat ttatcaagag 2940 ccatttaaaa atctgaaaac aggaaaatat gcaagaatga ggggtgccca cactaatgat 3000 gtaaaacaat taacagaggc agtgcaaaaa ataaccacag aaagcatagt aatatgggga 3060 aagactccta aatttaaact acccatacaa aaggaaacat gggaaacatg gtggacagag 3120 tattggcaag ccacctggat tcctgagtgg gagtttgtta atacccctcc tttagtgaaa 3180 ttatggtacc agttagagaa agaacccata gtaggagcag aaaccttcta tgtagatggg 3240 gcagctaaca gggagactaa attaggaaaa gcaggatatg ttactaacaa aggaagacaa 3300 aaggttgtcc ccctaactaa cacaacaaat cagaaaactg agttacaagc aatttatcta 3360 gctttgcagg attcaggatt agaagtaaac atagtaacag actcacaata tgcattagga 3420 atcattcaag cacaaccaga taaaagtgaa tcagagttag tcaatcaaat aatagagcag 3480 ttaataaaaa aggaaaaggt ctatctggca tgggtaccag cacacaaagg aattggagga 3540 aatgaacaag tagataaatt agtcagtgct ggaatcagga aaatactatt tttagatgga 3600 atagataagg cccaagatga acatgagaaa tatcacagta attggagagc aatggctagt 3660 gattttaacc tgccacctgt agtagcaaaa gaaatagtag ccagctgtga taaatgtcag 3720 ctaaaaggag aagccatgca tggacaagta gactgtagtc caggaatatg gcaactagat 3780 tgtacacatt tagaaggaaa agttatcctg gtagcagttc atgtagccag tggatatata 3840 gaagcagaag ttattccagc agaaacaggg caggaaacag catattttct tttaaaatta 3900 gcaggaagat ggccagtaaa aacaatacat acagacaatg gcagcaattt caccagtgct 3960 acggttaagg ccgcctgttg gtgggcggga atcaagcagg aatttggaat tccctacaat 4020 ccccaaagtc aaggagtagt agaatctatg aataaagaat taaagaaaat tataggacag 4080 gtaagagatc aggctgaaca tcttaagaca gcagtacaaa tggcagtatt catccacaat 4140 tttaaaagaa aaggggggat tggggggtac agtgcagggg aaagaatagt agacataata 4200 gcaacagaca tacaaactaa agaattacaa aaacaaatta caaaaattca aaattttcgg 4260 gtttattaca gggacagcag aaatccactt tggaaaggac cagcaaagct cctctggaaa 4320 ggtgaagggg cagtagtaat acaagataat agtgacataa aagtagtgcc aagaagaaaa 4380 gcaaagatca ttagggatta tggaaaacag atggcaggtg atgattgtgt ggcaagtaga 4440 caggatgagg attagaacat ggaaaagttt agtaaaacac catatgtatg tttcagggaa 4500 agctagggga tggttttata gacatcacta tgaaagccct catccaagaa taagttcaga 4560 agtacacatc ccactagggg atgctagatt ggtaataaca acatattggg gtctgcatac 4620 aggagaaaga gactggcatt tgggtcaggg agtctccata gaatggagga aaaagagata 4680 tagcacacaa gtagaccctg aactagcaga ccaactaatt catctgtatt actttgactg 4740 tttttcagac tctgctataa gaaaggcctt attaggacac atagttagcc ctaggtgtga 4800 atatcaagca ggacataaca aggtaggatc tctacaatac ttggcactag cagcattaat 4860 aacaccaaaa aagataaagc cacctttgcc tagtgttacg aaactgacag aggatagatg 4920 gaacaagccc cagaagacca agggccacag agggagccac acaatgaatg gacactagag 4980 cttttagagg agcttaagaa tgaagctgtt agacattttc ctaggatttg gctccatggc 5040 ttagggcaac atatctatga aacttatggg gatacttggg caggagtgga agccataata 5100 agaattctgc aacaactgct gtttatccat tttcagaatt gggtgtcgac atagcagaat 5160 aggcgttact cgacagagga gagcaagaaa tggagccagt agatcctaga ctagagccct 5220 ggaagcatcc aggaagtcag cctaaaactg cttgtaccaa ttgctattgt aaaaagtgtt 5280 gctttcattg ccaagtttgt ttcataacaa aagccttagg catctcctat ggcaggaaga 5340 agcggagaca gcgacgaaga cctcctcaag gcagtcagac tcatcaagtt tctctatcaa 5400 agcagtaagt agtacatgta atgcaaccta tacaaatagc aatagtagca ttagtagtag 5460 caataataat agcaatagtt gtgtggtcca tagtaatcat agaatatagg aaaatattaa 5520 gacaaagaaa aatagacagg ttaattgata gactaataga aagagcagaa gacagtggca 5580 atgagagtga aggagaaata tcagcacttg tggagatggg ggtggagatg gggcaccatg 5640 ctccttggga tgttgatgat ctgtagtgct acagaaaaat tgtgggtcac agtctattat 5700 ggggtacctg tgtggaagga agcaaccacc actctatttt gtgcatcaga tgctaaagca 5760 tatgatacag aggtacataa tgtttgggcc acacatgcct gtgtacccac agaccccaac 5820 ccacaagaag tagtattggt aaatgtgaca gaaaatttta acatgtggaa aaatgacatg 5880 gtagaacaga tgcatgagga tataatcagt ttatgggatc aaagcctaaa gccatgtgta 5940 aaattaaccc cactctgtgt tagtttaaag tgcactgatt tgaagaatga tactaatacc 6000 aatagtagta gcgggagaat gataatggag aaaggagaga taaaaaactg ctctttcaat 6060 atcagcacaa gcataagagg taaggtgcag aaagaatatg cattttttta taaacttgat 6120 ataataccaa tagataatga tactaccagc tatacgttga caagttgtaa cacctcagtc 6180 attacacagg cctgtccaaa ggtatccttt gagccaattc ccatacatta ttgtgccccg 6240 gctggttttg cgattctaaa atgtaataat aagacgttca atggaacagg accatgtaca 6300 aatgtcagca cagtacaatg tacacatgga attaggccag tagtatcaac tcaactgctg 6360 ttaaatggca gtctggcaga agaagaggta gtaattagat ctgccaattt cacagacaat 6420 gctaaaacca taatagtaca gctgaaccaa tctgtagaaa ttaattgtac aagacccaac 6480 aacaatacaa gaaaaagtat ccgtatccag agaggaccag ggagagcatt tgttacaata 6540 ggaaaaatag gaaatatgag acaagcacat tgtaacatta gtagagcaaa atggaataac 6600 actttaaaac agatagatag caaattaaga gaacaatttg gaaataataa aacaataatc 6660 tttaagcagt cctcaggagg ggacccagaa attgtaacgc acagttttaa ttgtggaggg 6720 gaatttttct actgtaattc aacacaactg tttaatagta cttggtttaa tagtacttgg 6780 agtactaaag ggtcaaataa cactgaagga agtgacacaa tcaccctccc atgcagaata 6840 aaacaaatta taaacatgtg gcaggaagta ggaaaagcaa tgtatgcccc tcccatcagt 6900 ggacaaatta gatgttcatc aaatattaca gggctgctat taacaagaga tggtggtaat 6960 agcaacaatg agtccgagat cttcagacct ggaggaggag atatgaggga caattggaga 7020 agtgaattat ataaatataa agtagtaaaa attgaaccat taggagtagc acccaccaag 7080 gcaaagagaa gagtggtgca gagagaaaaa agagcagtgg gaataggagc tttgttcctt 7140 gggttcttgg gagcagcagg aagcactatg ggcgcagcgt caatgacgct gacggtacag 7200 gccagacaat tattgtctgg tatagtgcag cagcagaaca atttgctgag ggctattgag 7260 gcgcaacagc atctgttgca actcacagtc tggggcatca agcagctcca ggcaagaatc 7320 ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg ttgctctgga 7380 aaactcattt gcaccactgc tgtgccttgg aatgctagtt ggagtaataa atctctggaa 7440 cagatttgga ataacatgac ctggatggag tgggacagag aaattaacaa ttacacaagc 7500 ttaatacact ccttaattga agaatcgcaa aaccagcaag aaaagaatga acaagaatta 7560 ttggaattag ataaatgggc aagtttgtgg aattggttta acataacaaa ttggctgtgg 7620 tatataaaat tattcataat gatagtagga ggcttggtag gtttaagaat agtttttgct 7680 gtactttctg tagtgaatag agttaggcag ggatattcac cattatcgtt tcagacccac 7740 ctcccaatcc cgaggggacc cgacaggccc gaaggaatag aagaagaagg tggagagaga 7800 gacagagaca gatccattcg attagtgaac ggatccttag cacttatctg ggacgatctg 7860 cggagcctgt gcctcttcag ctaccaccgc ttgagagact tactcttgat tgtaacgagg 7920 attgtggaac ttctgggacg cagggggtgg gaagccctca aatattggtg gaatctccta 7980 cagtattgga gtcaggagct aaagaatagt gctgttagct tgctcaatgc cacagctata 8040 gcagtagctg aggggacaga tagggttata gaagtagtac aaggagctta tagagctatt 8100 cgccacatac ctagaagaat aagacagggc ttggaaagga ttttgctata agatgggtgg 8160 caagtggtca aaaagtagtg tggttggatg gcctgctgta agggaaagaa tgagacgagc 8220 tgagccagca gcagatgggg tgggagcagc atctcgagac ctagaaaaac atggagcaat 8280 cacaagtagc aacacagcag ctaacaatgc tgattgtgcc tggctagaag cacaagagga 8340 ggaggaggtg ggttttccag tcacacctca ggtaccttta agaccaatga cttacaaggc 8400 agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc taattcactc 8460 ccaacgaaga caagatatcc ttgatctgtg gatctaccac acacaaggct acttccctga 8520 ttagcagaac tacacaccag ggccagggat cagatatcca ctgacctttg gatggtgcta 8580 caagctagta ccagttgagc cagagaagtt agaagaagcc aacaaaggag agaacaccag 8640 cttgttacac cctgtgagcc tgcatggaat ggatgacccg gagagagaag tgttagagtg 8700 gaggtttgac agccgcctag catttcatca catggcccga gagctgcatc cggagtactt 8760 caagaactgc tgacatcgag cttgctacaa gggactttcc gctggggact ttccagggag 8820 gcgtggcctg ggcgggactg gggagtggcg agccctcaga tcctgcatat aagcagctgc 8880 tttttgcctg tactgggtct ctctggttag accagatctg agcctgggag ctc 8933 5 5362 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(5362) /standard_name= "Clone BH5" /note= "Corresponds to nucleotide positions 222 to 5585 in figure 3 of US 06/693,866" 5 gagctctctc gacgcaggac tcggcttgcg agcgcgcacg gcaagaggcg aggggcggcg 60 actggtgagt acgccaaaaa ttttgactag cggaggctag aaggagagag atgggtgcga 120 gagcgtcagt attaagcggg ggagaattag atcgatggga aaaaattcgg ttaaggccag 180 ggggaaagaa aaaatataaa ttaaaacata tagtatgggc aagcagggag ctagaacgat 240 tcgcagttaa tcctggcctg ttagaaacat cagaaggctg tagacaaata ctgggacagc 300 tacaaccatc ccttcagaca ggatcagaag aacttagatc attatataat acagtagcaa 360 ccctctattg tgtgcatcaa aggatagaga taaaagacac caaggaagct ttagacaaga 420 tagaggaaga gcaaaacaaa agtaagaaaa aagcacagca agcagcagct gacacaggac 480 acagcagtca ggtcagccaa aattacccta tagtgcagaa catccagggg caaatggtac 540 atcaggccat atcacctaga actttaaatg catgggtaaa agtagtagaa gagaaggctt 600 tcagcccaga agtgataccc atgttttcag cattatcaga aggagccacc ccacaagatt 660 taaacaccat gctaaacaca gtggggggac atcaagcagc catgcaaatg ttaaaagaga 720 ccatcaatga ggaagctgca gaatgggata gagtgcatcc agtgcatgca gggcctatcg 780 caccaggcca gatgagagaa ccaaggggaa gtgacatagc aggaactact agtacccttc 840 aggaacaaat aggatggatg acaaataatc cacctatccc agtaggagaa atttataaaa 900 gatggataat cctgggatta aataaaatag taaggatgta tagtcctacc agcattctgg 960 acataagaca aggaccaaag gaacccttta gagactatgt agaccggttc tataaaactc 1020 taagagccga gcaagcttca caggaagtaa aaaattggat gacagaaacc ttgttggtcc 1080 aaaatgcgaa cccagattgt aagactattt taaaagcatt gggaccagcg gctacactag 1140 aagaaatgat gacagcatgt cagggagtag gaggacccgg ccataaggca agagttttgg 1200 ctgaagcaat gagccaagta acaaattcaa ctaccataat gatgcaaaga ggcaatttta 1260 ggaaccaaag aaaaattgtt aagtgtttca attgtggcaa agaagggcac atagcaagaa 1320 attgcaaggc ccctagaaaa aagggctgtt ggaaatgtgg aaaggaagga caccaaatga 1380 aagattgtac tgagagacag gctaattttt tagggaagat ctggccttcc tacaagggaa 1440 ggccagggaa ttttcttcag agcagaccag agccaacagc cccaccattt cttcagagca 1500 gaccagagcc aacagcccca ccagaagaga gcttcaggtc tggggtagag acaacaactc 1560 cccctcagaa gcaggagccg atagacaagg aactgtatcc tttaacttcc ctcagatcac 1620 tctttggcaa cgacccctcg tcacaataaa gatagggggg caactaaagg aagctctatt 1680 agatacagga gcagatgata cagtattaga agaaatgagt ttgccaggaa gatggaaacc 1740 aaaaatgata gggggaattg gaggttttat caaagtaaga cagtatgatc agatactcat 1800 agaaatctgt ggacataaag ctataggtac agtattagta ggacctacac ctgtcaacat 1860 aattggaaga aatctgttga ctcagattgg ttgcacttta aattttccca ttagtcctat 1920 tgaaactgta ccagtaaaat taaagccagg aatggatggc ccaaaagtta aacaatggcc 1980 attgacagaa gaaaaaataa aagcattagt agaaatttgt acagaaatgg aaaaggaagg 2040 gaaaatttca aaaattgggc ctgaaaatcc atacaatact ccagtatttg ccataaagaa 2100 aaaagacagt actaaatgga gaaaattagt agatttcaga gaacttaata ggagaactca 2160 agacttctgg gaagttcaat tgggaatacc acatcccgca gggttaaaaa agaaaaaatc 2220 agtaacagta ctggatgtgg gtgatgcata tttttcagtt cccttagatg aagacttcag 2280 gaagtatact gcatttacca tacctagtat aaataatgag acaccaggga gtggatatca 2340 gtacaatgtg cttccacagg gatggaaagg atcaccagca atattccaaa gtagcatgac 2400 aaaaatctta gagcctttta gaaaacaaaa tccagacata gttatttatc aatacatgga 2460 tgatttgtat gtaggatctg acttagaaat agggcagcat agaacaaaaa tagaggagct 2520 gagacaacat ctgttgaggt ggggatttac cacaccagac aaaaaacatc agaaagaacc 2580 tccattcctt tggatgggtt atgaactcca tcctgataaa tggacgatac agcctatagt 2640 gctgccagaa aaagacagct ggactgtcaa tgacatacag aagttagtgg gaaaattgaa 2700 ttgggcaagt cagatttatc cagggattaa agtaaggcaa ttatgtaaac tccttagagg 2760 aaccaaagca ctaacagaag taataccact aacagaagaa gcagagctag aactggcaga 2820 aaacagagag attctaaaag aaccagtaca tggagtgtat tatgacccat caaaagactt 2880 aatagcagaa atacagaagc aggggcaagg ccaatggaca tatcaaattt atcaagagcc 2940 atttaaaaat ctgaaaacag gaaaatatgc aagaatgagg ggtgcccaca ctaatgatgt 3000 aaaacaatta acagaggcag tgcaaaaaat aaccacagaa agcatagtaa tatggggaaa 3060 gactcctaaa tttaaactac ccatacaaaa agaaacatgg gaaacatggt ggacagagta 3120 ttggcaagcc acctggattc ctgagtggga gtttgttaat acccctcctt tagtgaaatt 3180 atggtaccag ttagagaaag aacccatagt aggagcagaa accttctatg tagatggggc 3240 agctagcagg gagactaaat taggaaaagc aggatatgtt actaatagag gaagacaaaa 3300 agttgtcacc ctaactcaca caacaaatca gaagactgaa ttacaagcaa ttcatctagc 3360 tttgcaggat tcgggattag aagtaaatat agtaacagac tcacaatatg cattaggaat 3420 cattcaagca caaccagata aaagtgaatc agagttagtc aatcaaataa tagagcagtt 3480 aataaaaaag gaaaaggtct atctggcatg ggtaccagca cacaaaggaa ttggaggaaa 3540 tgaacaagta gataaattag tcagtgctgg aatcaggaaa atactatttt tagatggaat 3600 agataaggcc caagaagaac atgagaaata tcacagtaat tggagagcaa tggctagtga 3660 ttttaacctg ccacctgtag tagcaaaaga aatagtagcc agctgtgata aatgtcagct 3720 aaaaggagaa gccatgcatg gacaagtaga ctgtagtcca ggaatatggc aactagattg 3780 tacacattta gaaggaaaag ttatcctggt agcagttcat gtagccagtg gatatataga 3840 agcagaagtt attccagcag aaacagggca ggaaacagca tattttcttt taaaattagc 3900 aggaagatgg ccagtaaaaa caatacatac agacaatggc agcaatttca ccagtgctac 3960 ggttaaggcc

gcctgttggt gggcgggaat caagcaggaa tttggaattc cctacaatcc 4020 ccaaagtcaa ggagtagtag aatctatgaa taaagaatta aagaaaatta taggacaggt 4080 aagagatcag gctgaacatc ttaagacagc agtacaaatg gcagtattca tccacaattt 4140 taaaagaaaa ggggggattg gggggtacag tgcaggggaa agaatagtag acataatagc 4200 aacagacata caaactaaag aattacaaaa acaaattaca aaaattcaaa attttcgggt 4260 ttattacagg gacagcagaa atccactttg gaaaggacca gcaaagctcc tctggaaagg 4320 tgaaggggca gtagtaatac aagataatag tgacataaaa gtagtgccaa gaagaaaagc 4380 aaagatcatt agggattatg gaaaacagat ggcaggtgat gattgtgtgg caagtagaca 4440 ggatgaggat tagaacatgg aaaagtttag taaaacaccg tatgtatgtt tcagggaaag 4500 ctaggggatg gttttataga catcactatg aaagccctca tccaagaata agttcagaag 4560 tacacatccc actaggggat gctagattgg taataacaac atattggggt ctgcatacag 4620 gagaaagaga ctggcatttg ggtcagggag tctccataga atggaggaaa aggagatata 4680 gcacacaagt agaccctgaa ctagcagacc aactaattca tctgcattac tttgattgtt 4740 tttcagactc tgctataaga aaggccttat taggacacat agttagccct aggtgtgaat 4800 atcaagcagg acataacaag gtaggatctc tacaatactt ggcactagca gcattaataa 4860 caccaaaaaa ggtaaagcca cctttgccta gtgttacgaa actgacagag gatagatgga 4920 acaagcccca gaagaccaag ggccacagag gaagccacac aatgaatgga cactagagct 4980 tttagaggag cttaagaatg aagctgttag acattttcct aggatttggc tccatggctt 5040 agggcaacat atctatgaaa cttatgggga tacttgggca ggagtggaag ccataataag 5100 aattctgcaa caactgctgt ttatccattt tcagaattgg gtgtcgacat agcagaatag 5160 gcgttactca acagaggaga gcaagaaatg gagccagtag atcctagact agagccctgg 5220 aagcatccag gaagtcagcc taaaactgct tgtaccactt gctattgtaa aaagtgttgc 5280 tttcattgcc aagtttgttt cataacaaaa gccttaggca tctcctatgg caggaagaag 5340 cggagacagc gacgaagagc tc 5362 6 3563 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(3563) /standard_name= "Clone BH8" /note= "Corresponds to nucleotide positions 5580 to 9154 in figure 3 of US 06/693,866" 6 gagctcatcg aagcagtcag actcatcaag tttctctatc aaagcagtaa gtagtacatg 60 taacgcaacc tataccaata gtaacaatag tagccttagc agtagcaata ataatagcaa 120 tagttgtgtg gtccatagta atcatagaat ataggaaaat attaagacaa agaaaaatag 180 acaggttaat tgatagacta atagaaagag cagaagacag tggcaatgag agtgaaggag 240 aaatatcagc acttgtggag atgggggtgg agatggggca ccatgctcct tgggatgttg 300 atgatctgta gtgctacaga aaaattgtgg gtcacagtct attttggggt acctgtgtgg 360 aaggaagcaa ccaccactct attttgtgca tcagatgcta aagcatatga tacagaggta 420 cataatgttt gggccacaca tgcctgtgta cccacagacc ccaacccaca agaagtagta 480 ttggtaaatg tgacagaaaa ttttaacatg tggaaaaatg acatggtaga acagatgcat 540 gaggatataa tcagtttatg ggatcaaagc ctaaagccat gtgtaaaatt aaccccactc 600 tgtgttagtt taaagtgcac tgatttgaag aatgatacta ataccaatag tagtagcggg 660 agaatgataa tggagaaagg agagataaaa aactgctctt tcaatatcag cacaagcaaa 720 agaggtaagg tgcagaaaga atatgcattt ttttataaac ttgatataat accaatagat 780 aatgatacta ccagctatac gttgacaagt tgtaacacct cagtcattac acaggcctgt 840 ccaaaggtat cctttgagcc aattcccata cattattgtg ccccggctgg ttttgcgatt 900 ctaaaatgta ataataagac gttcaatgga acaggaccat gtacaaatgt cagcacagta 960 caatgtacac atggaattag gccagtagta tcaactcaac tgctgttaaa tggcagtctg 1020 gcagaagaag aggtagtaat tagatctgtc aatttcacgg acaatgctaa aaccataata 1080 gtacagctgg acacatctgt agaaattaat tgtacaagac ccaacaacaa tacaagaaaa 1140 aaaatccgta tccagagggg accagggaga gcatttgtta caataggaaa aataggaaat 1200 atgagacaag cacattgtaa cattagtaga gcaaaatgga atgccacttt aaaacagata 1260 gatagcaaat taagagaaca atttggaaat aataaaacaa taatctttaa gcagtcctca 1320 ggaggggacc cagaaattgt aacgcacagt tttaattgtg gaggggaatt tttctactgt 1380 aattcaacac aactgtttaa tagtacttgg agtactaaag ggtcaaataa cactgaagga 1440 agtgacacaa tcaccctccc atgcagaata aaacaaatta taaacatgtg gcaggaagta 1500 ggaaaagcaa tgtatgcccc tcccatcagt ggacaaatta gatgttcatc aaatattaca 1560 gggctgctat taacaagaga tggtggtaat agcaacaatg agtccgagat cttcagacct 1620 ggaggaggag atatgaggga caattggaga agtgaattat ataaatataa agtagtaaaa 1680 attgaaccat taggagtagc acccaccaag gcaaagagaa gagtggtgca gagagaaaaa 1740 agagcagtgg gaataggagc tttgttcctt gggttcttgg gagcagcagg aagcactatg 1800 ggcgcagcgt caatgacgct gacggtacag gccagacaat tattgtctgg tatagtgcag 1860 cagcagaaca atttgctgag ggctattgag ggccaacagc atctgttgca actcacagtc 1920 tggggcatca agcagctcca ggcaagaatc ctggctgtgg aaagatacct aaaggatcaa 1980 cagctcctgg ggatttgggg ttgctctgga aaactcattt gcaccactgc tgtgccttgg 2040 aatgctagtt ggagtaataa atctctggaa cagatttgga ataacatgac ctggatggag 2100 tgggacagag aaattaacaa ttacacaagc ttaatacact ccttaattga agaatcgcaa 2160 aaccagcaag aaaagaatga acaagaatta ttggaattag ataaatgggc aagtttgtgg 2220 aattggttta acataacaaa ttggctgtgg tatataaaat tattcataat gatagtagga 2280 ggcttggtag gtttaagaat agtttttgct gtactttcta tagtgaatag agttaggcag 2340 ggatattcac cattatcgtt tcagacccac ctcccaaacc cgaggggacc cgacaggccc 2400 gaaggaatag aagaagaagg tggagagaga gacagagaca gatccattcg attagtgaac 2460 ggatccttag cacttatctg ggacgatctg cggagcctgt gcctcttcag ctaccaccgc 2520 ttgagagact tactcttgat tgtaacgagg attgtggaac ttctgggacg cagggggtgg 2580 gaagccctca aatattggtg gaatctccta cagtattgga gtcaggaact aaagaatagt 2640 gctgttaact tgctcaatgc cacagctata gcagtagctg aggggacaga tagggttata 2700 gaattagtac aagcagctta tagagccatt cgccacatac ctagaagaat aagacagggc 2760 ttggaaagga ttttgctata agatgggtgg caagtggtca aaaagtagtg tggttggatg 2820 gcctgctgta agggaaagaa tgagacgagc tgagccagca gcagatgggg tgggagcagt 2880 atctcgagac ctagaaaaac atggagcaat cacaagtagc aatacagcag ctaccaatgc 2940 cgattgtgct tggctagaag cacaagagga ggaggaggtg ggttttccag tcacacctca 3000 ggtaccttta agaccaatga cttacaaggc agctgtagat cttagccact ttttaaaaga 3060 aaagggggga ctggaagggc taattcactc ccaacgaaga caagatatcc ttgatctgtg 3120 gatccaccac acacaaggct acttccctga ttggcagaac tacacaccag ggccaggagt 3180 cagatatcca ctgacctttg gatggtgcta caagctagta ccagttgagc cagagaagta 3240 agaagaagcc aataaaggag agaacaccag cttgttacac cctgtgagcc tgcatggaat 3300 ggatgaccct gagagagaag tgttagagtg gaggtttgac agccgcctag catttcatca 3360 catggcccga gagctgcatc cggagtactt caagaactgc tgatatcgag cttgctacaa 3420 gggactttcc gctggggact ttccagggag gcgtggcctg ggcgggactg gggagtggcg 3480 agccctcaga tcctgcatat aagcagctgc tttttgcctg tactgggtct ctctggttag 3540 accagatctg agcctgggag ctc 3563 7 142 DNA T cell leukemia-lymphoma virus (HTLV) misc_feature (1)..(142) /standard_name= "Clone HXB2" /note= "Corresponds to nucleotide positions 9155 to 9296 in figure 3 of US 06/693,866" 7 tctggctagc tagggaaccc actgcttaag cctcaataaa gcttgccttg agtgcttcaa 60 gtagtgtgtg cccgtctgtt gtgtgactct ggtaactaga gatccctcag acccttttag 120 tcagtgtgga aaatctctag ca 142 8 512 PRT T cell leukemia-lymphoma virus (HTLV) MISC_FEATURE (1)..(512) /note= "gag protein of HTLV-III" 8 Met Gly Ala Arg Ala Ser Val Leu Ser Gly Gly Glu Leu Asp Arg Trp 1 5 10 15 Glu Lys Ile Arg Leu Arg Pro Gly Gly Lys Lys Lys Tyr Lys Leu Lys 20 25 30 His Ile Val Trp Ala Ser Arg Glu Leu Glu Arg Phe Ala Val Asn Pro 35 40 45 Gly Leu Leu Glu Thr Ser Glu Gly Cys Arg Gln Ile Leu Gly Gln Leu 50 55 60 Gln Pro Ser Leu Gln Thr Gly Ser Glu Glu Leu Arg Ser Leu Tyr Asn 65 70 75 80 Thr Val Ala Thr Leu Tyr Cys Val His Gln Arg Ile Glu Ile Lys Asp 85 90 95 Thr Lys Glu Ala Leu Asp Lys Ile Glu Glu Glu Gln Asn Lys Ser Lys 100 105 110 Lys Lys Ala Gln Gln Ala Ala Ala Asp Thr Gly His Ser Ser Gln Val 115 120 125 Ser Gln Asn Tyr Pro Ile Val Gln Asn Ile Gln Gly Gln Met Val His 130 135 140 Gln Ala Ile Ser Pro Arg Thr Leu Asn Ala Trp Val Lys Val Val Glu 145 150 155 160 Glu Lys Ala Phe Ser Pro Glu Val Ile Pro Met Phe Ser Ala Leu Ser 165 170 175 Glu Gly Ala Thr Pro Gln Asp Leu Asn Thr Met Leu Asn Thr Val Gly 180 185 190 Gly His Gln Ala Ala Met Gln Met Leu Lys Glu Thr Ile Asn Glu Glu 195 200 205 Ala Ala Glu Trp Asp Arg Val His Pro Val His Ala Gly Pro Ile Ala 210 215 220 Pro Gly Gln Met Arg Glu Pro Arg Gly Ser Asp Ile Ala Gly Thr Thr 225 230 235 240 Ser Thr Leu Gln Glu Gln Ile Gly Trp Met Thr Asn Asn Pro Pro Ile 245 250 255 Pro Val Gly Glu Ile Tyr Lys Arg Trp Ile Ile Leu Gly Leu Asn Lys 260 265 270 Ile Val Arg Met Tyr Ser Pro Thr Ser Ile Leu Asp Ile Arg Gln Gly 275 280 285 Pro Lys Glu Pro Phe Arg Asp Tyr Val Asp Arg Phe Tyr Lys Thr Leu 290 295 300 Arg Ala Glu Gln Ala Ser Gln Glu Val Lys Asn Trp Met Thr Glu Thr 305 310 315 320 Leu Leu Val Gln Asn Ala Asn Pro Asp Cys Lys Thr Ile Leu Lys Ala 325 330 335 Leu Gly Pro Ala Ala Thr Leu Glu Glu Met Met Thr Ala Cys Gln Gly 340 345 350 Val Gly Gly Pro Gly His Lys Ala Arg Val Leu Ala Glu Ala Met Ser 355 360 365 Gln Val Thr Asn Thr Ala Thr Ile Met Met Gln Arg Gly Asn Phe Arg 370 375 380 Asn Gln Arg Lys Met Val Lys Cys Phe Asn Cys Gly Lys Glu Gly His 385 390 395 400 Thr Ala Arg Asn Cys Arg Ala Pro Arg Lys Lys Gly Cys Trp Lys Cys 405 410 415 Gly Lys Glu Gly His Gln Met Lys Asp Cys Thr Glu Arg Gln Ala Asn 420 425 430 Phe Leu Gly Lys Ile Trp Pro Ser Tyr Lys Gly Arg Pro Gly Asn Phe 435 440 445 Leu Gln Ser Arg Pro Glu Pro Thr Ala Pro Pro Phe Leu Gln Ser Arg 450 455 460 Pro Glu Pro Thr Ala Pro Pro Glu Glu Ser Phe Arg Ser Gly Val Glu 465 470 475 480 Thr Thr Thr Pro Pro Gln Lys Gln Glu Pro Ile Asp Lys Glu Leu Tyr 485 490 495 Pro Leu Thr Ser Leu Arg Ser Leu Phe Gly Asn Asp Pro Ser Ser Gln 500 505 510 9 1015 PRT T cell leukemia-lymphoma virus (HTLV) MISC_FEATURE (1)..(1015) /note= "pol protein of HTLV-III" 9 Phe Phe Arg Glu Asp Leu Ala Phe Leu Gln Gly Lys Ala Arg Glu Phe 1 5 10 15 Ser Ser Glu Gln Thr Arg Ala Asn Ser Pro Thr Ile Ser Ser Glu Gln 20 25 30 Thr Arg Ala Asn Ser Pro Thr Arg Arg Glu Leu Gln Val Trp Gly Arg 35 40 45 Asp Asn Asn Ser Pro Ser Glu Ala Gly Ala Asp Arg Gln Gly Thr Val 50 55 60 Ser Phe Asn Phe Pro Gln Ile Thr Leu Trp Gln Arg Pro Leu Val Thr 65 70 75 80 Ile Lys Ile Gly Gly Gln Leu Lys Glu Ala Leu Leu Asp Thr Gly Ala 85 90 95 Asp Asp Thr Val Leu Glu Glu Met Ser Leu Pro Gly Arg Trp Lys Pro 100 105 110 Lys Met Ile Gly Gly Ile Gly Gly Phe Ile Lys Val Arg Gln Tyr Asp 115 120 125 Gln Ile Leu Ile Glu Ile Cys Gly His Lys Ala Ile Gly Thr Val Leu 130 135 140 Val Gly Pro Thr Pro Val Asn Ile Ile Gly Arg Asn Leu Leu Thr Gln 145 150 155 160 Ile Gly Cys Thr Leu Asn Phe Pro Ile Ser Pro Ile Glu Thr Val Pro 165 170 175 Val Lys Leu Lys Pro Gly Met Asp Gly Pro Lys Val Lys Gln Trp Pro 180 185 190 Leu Thr Glu Glu Lys Ile Lys Ala Leu Val Glu Ile Cys Thr Glu Met 195 200 205 Glu Lys Glu Gly Lys Ile Ser Lys Ile Gly Pro Glu Asn Pro Tyr Asn 210 215 220 Thr Pro Val Phe Ala Ile Lys Lys Lys Asp Ser Thr Lys Trp Arg Lys 225 230 235 240 Leu Val Asp Phe Arg Glu Leu Asn Lys Arg Thr Gln Asp Phe Trp Glu 245 250 255 Val Gln Leu Gly Ile Pro His Pro Ala Gly Leu Lys Lys Lys Lys Ser 260 265 270 Val Thr Val Leu Asp Val Gly Asp Ala Tyr Phe Ser Val Pro Leu Asp 275 280 285 Glu Asp Phe Arg Lys Tyr Thr Ala Phe Thr Ile Pro Ser Ile Asn Asn 290 295 300 Glu Thr Pro Gly Ile Arg Tyr Gln Tyr Asn Val Leu Pro Gln Gly Trp 305 310 315 320 Lys Gly Ser Pro Ala Ile Phe Gln Ser Ser Met Thr Lys Ile Leu Glu 325 330 335 Pro Phe Lys Lys Gln Asn Pro Asp Ile Val Ile Tyr Gln Tyr Met Asp 340 345 350 Asp Leu Tyr Val Gly Ser Asp Leu Glu Ile Gly Gln His Arg Thr Lys 355 360 365 Ile Glu Glu Leu Arg Gln His Leu Leu Arg Trp Gly Leu Thr Thr Pro 370 375 380 Asp Lys Lys His Gln Lys Glu Pro Pro Phe Leu Trp Met Gly Tyr Glu 385 390 395 400 Leu His Pro Asp Lys Trp Thr Val Gln Pro Ile Val Leu Pro Glu Lys 405 410 415 Asp Ser Trp Thr Val Asn Asp Ile Gln Lys Leu Val Gly Lys Leu Asn 420 425 430 Trp Ala Ser Gln Ile Tyr Pro Gly Ile Lys Val Arg Gln Leu Cys Lys 435 440 445 Leu Leu Arg Gly Thr Lys Ala Leu Thr Glu Val Ile Pro Leu Thr Glu 450 455 460 Glu Ala Glu Leu Glu Leu Ala Glu Asn Arg Glu Ile Leu Lys Glu Pro 465 470 475 480 Val His Gly Val Tyr Tyr Asp Pro Ser Lys Asp Leu Ile Ala Glu Ile 485 490 495 Gln Lys Gln Gly Gln Gly Gln Trp Thr Tyr Gln Ile Tyr Gln Glu Pro 500 505 510 Phe Lys Asn Leu Lys Thr Gly Lys Tyr Ala Arg Met Arg Gly Ala His 515 520 525 Thr Asn Asp Val Lys Gln Leu Thr Glu Ala Val Gln Lys Ile Thr Thr 530 535 540 Glu Ser Ile Val Ile Trp Gly Lys Thr Pro Lys Phe Lys Leu Pro Ile 545 550 555 560 Gln Lys Glu Thr Trp Glu Thr Trp Trp Thr Glu Tyr Trp Gln Ala Thr 565 570 575 Trp Ile Pro Glu Trp Glu Phe Val Asn Thr Pro Pro Leu Val Lys Leu 580 585 590 Trp Tyr Gln Leu Glu Lys Glu Pro Ile Val Gly Ala Glu Thr Phe Tyr 595 600 605 Val Asp Gly Ala Ala Asn Arg Glu Thr Lys Leu Gly Lys Ala Gly Tyr 610 615 620 Val Thr Asn Lys Gly Arg Gln Lys Val Val Pro Leu Thr Asn Thr Thr 625 630 635 640 Asn Gln Lys Thr Glu Leu Gln Ala Ile Tyr Leu Ala Leu Gln Asp Ser 645 650 655 Gly Leu Glu Val Asn Ile Val Thr Asp Ser Gln Tyr Ala Leu Gly Ile 660 665 670 Ile Gln Ala Gln Pro Asp Lys Ser Glu Ser Glu Leu Val Asn Gln Ile 675 680 685 Ile Glu Gln Leu Ile Lys Lys Glu Lys Val Tyr Leu Ala Trp Val Pro 690 695 700 Ala His Lys Gly Ile Gly Gly Asn Glu Gln Val Asp Lys Leu Val Ser 705 710 715 720 Ala Gly Ile Arg Lys Ile Leu Phe Leu Asp Gly Ile Asp Lys Ala Gln 725 730 735 Asp Glu His Glu Lys Tyr His Ser Asn Trp Arg Ala Met Ala Ser Asp 740 745 750 Phe Asn Leu Pro Pro Val Val Ala Lys Glu Ile Val Ala Ser Cys Asp 755 760 765 Lys Cys Gln Leu Lys Gly Glu Ala Met His Gly Gln Val Asp Cys Ser 770 775 780 Pro Gly Ile Trp Gln Leu Asp Cys Thr His Leu Glu Gly Lys Val Ile 785 790 795 800 Leu Val Ala Val His Val Ala Ser Gly Tyr Ile Glu Ala Glu Val Ile 805 810 815 Pro Ala Glu Thr Gly Gln Glu Thr Ala Tyr Phe Leu Leu Lys Leu Ala 820 825 830 Gly Arg Trp Pro Val Lys Thr Ile His Thr Asp Asn Gly Ser Asn Phe 835 840 845 Thr Ser Ala Thr Val Lys Ala Ala Cys Trp Trp Ala Gly Ile Lys Gln 850 855 860 Glu Phe Gly Ile Pro Tyr Asn Pro Gln Ser Gln Gly Val Val Glu Ser 865 870 875 880 Met Asn Lys Glu Leu Lys Lys Ile Ile Gly Gln Val Arg Asp Gln Ala 885 890 895 Glu His Leu Lys Thr Ala Val Gln Met Ala Val Phe Ile His Asn Phe 900 905 910 Lys Arg Lys Gly Gly Ile Gly Gly Tyr Ser Ala Gly Glu Arg Ile Val 915 920 925 Asp Ile Ile Ala Thr Asp Ile Gln Thr Lys Glu Leu Gln Lys Gln Ile 930 935 940 Thr Lys Ile Gln Asn Phe Arg Val Tyr Tyr Arg Asp Ser Arg Asn Pro 945 950 955 960 Leu Trp Lys Gly Pro Ala Lys Leu Leu Trp Lys Gly Glu Gly Ala Val 965 970 975 Val Ile Gln Asp Asn Ser Asp Ile Lys Val Val Pro Arg Arg Lys Ala 980 985 990 Lys Ile Ile Arg Asp Tyr Gly Lys Gln Met Ala Gly Asp Asp Cys Val

995 1000 1005 Ala Ser Arg Gln Asp Glu Asp 1010 1015 10 203 PRT T cell leukemia-lymphoma virus (HTLV) MISC_FEATURE (1)..(203) /note= "sor protein of HTLV-III" 10 Cys Gln Glu Glu Lys Gln Arg Ser Leu Gly Ile Met Glu Asn Arg Trp 1 5 10 15 Gln Val Met Ile Val Trp Gln Val Asp Arg Met Arg Ile Arg Thr Trp 20 25 30 Lys Ser Leu Val Lys His His Met Tyr Val Ser Gly Lys Ala Arg Gly 35 40 45 Trp Phe Tyr Arg His His Tyr Glu Ser Pro His Pro Arg Ile Ser Ser 50 55 60 Glu Val His Ile Pro Leu Gly Asp Ala Arg Leu Val Ile Thr Thr Tyr 65 70 75 80 Trp Gly Leu His Thr Gly Glu Arg Asp Trp His Leu Gly Gln Gly Val 85 90 95 Ser Ile Glu Trp Arg Lys Lys Arg Tyr Ser Thr Gln Val Asp Pro Glu 100 105 110 Leu Ala Asp Gln Leu Ile His Leu Tyr Tyr Phe Asp Cys Phe Ser Asp 115 120 125 Ser Ala Ile Arg Lys Ala Leu Leu Gly His Ile Val Ser Pro Arg Cys 130 135 140 Glu Tyr Gln Ala Gly His Asn Lys Val Gly Ser Leu Gln Tyr Leu Ala 145 150 155 160 Leu Ala Ala Leu Ile Thr Pro Lys Lys Ile Lys Pro Pro Leu Pro Ser 165 170 175 Val Thr Lys Leu Thr Glu Asp Arg Trp Asn Lys Pro Gln Lys Thr Lys 180 185 190 Gly His Arg Gly Ser His Thr Met Asn Gly His 195 200 11 863 PRT T cell leukemia-lymphoma virus (HTLV) MISC_FEATURE (1)..(863) /note= "env protein of HTLV-III" 11 Lys Glu Gln Lys Thr Val Ala Met Arg Val Lys Glu Lys Tyr Gln His 1 5 10 15 Leu Trp Arg Trp Gly Trp Arg Trp Gly Thr Met Leu Leu Gly Met Leu 20 25 30 Met Ile Cys Ser Ala Thr Glu Lys Leu Trp Val Thr Val Tyr Tyr Gly 35 40 45 Val Pro Val Trp Lys Glu Ala Thr Thr Thr Leu Phe Cys Ala Ser Asp 50 55 60 Ala Lys Ala Tyr Asp Thr Glu Val His Asn Val Trp Ala Thr His Ala 65 70 75 80 Cys Val Pro Thr Asp Pro Asn Pro Gln Glu Val Val Leu Val Asn Val 85 90 95 Thr Glu Asn Phe Asn Met Trp Lys Asn Asp Met Val Glu Gln Met His 100 105 110 Glu Asp Ile Ile Ser Leu Trp Asp Gln Ser Leu Lys Pro Cys Val Lys 115 120 125 Leu Thr Pro Leu Cys Val Ser Leu Lys Cys Thr Asp Leu Lys Asn Asp 130 135 140 Thr Asn Thr Asn Ser Ser Ser Gly Arg Met Ile Met Glu Lys Gly Glu 145 150 155 160 Ile Lys Asn Cys Ser Phe Asn Ile Ser Thr Ser Ile Arg Gly Lys Val 165 170 175 Gln Lys Glu Tyr Ala Phe Phe Tyr Lys Leu Asp Ile Ile Pro Ile Asp 180 185 190 Asn Asp Thr Thr Ser Tyr Thr Leu Thr Ser Cys Asn Thr Ser Val Ile 195 200 205 Thr Gln Ala Cys Pro Lys Val Ser Phe Glu Pro Ile Pro Ile His Tyr 210 215 220 Cys Ala Pro Ala Gly Phe Ala Ile Leu Lys Cys Asn Asn Lys Thr Phe 225 230 235 240 Asn Gly Thr Gly Pro Cys Thr Asn Val Ser Thr Val Gln Cys Thr His 245 250 255 Gly Ile Arg Pro Val Val Ser Thr Gln Leu Leu Leu Asn Gly Ser Leu 260 265 270 Ala Glu Glu Glu Val Val Ile Arg Ser Ala Asn Phe Thr Asp Asn Ala 275 280 285 Lys Thr Ile Ile Val Gln Leu Asn Gln Ser Val Glu Ile Asn Cys Thr 290 295 300 Arg Pro Asn Asn Asn Thr Arg Lys Ser Ile Arg Ile Gln Arg Gly Pro 305 310 315 320 Gly Arg Ala Phe Val Thr Ile Gly Lys Ile Gly Asn Met Arg Gln Ala 325 330 335 His Cys Asn Ile Ser Arg Ala Lys Trp Asn Asn Thr Leu Lys Gln Ile 340 345 350 Asp Ser Lys Leu Arg Glu Gln Phe Gly Asn Asn Lys Thr Ile Ile Phe 355 360 365 Lys Gln Ser Ser Gly Gly Asp Pro Glu Ile Val Thr His Ser Phe Asn 370 375 380 Cys Gly Gly Glu Phe Phe Tyr Cys Asn Ser Thr Gln Leu Phe Asn Ser 385 390 395 400 Thr Trp Phe Asn Ser Thr Trp Ser Thr Lys Gly Ser Asn Asn Thr Glu 405 410 415 Gly Ser Asp Thr Ile Thr Leu Pro Cys Arg Ile Lys Gln Ile Ile Asn 420 425 430 Met Trp Gln Glu Val Gly Lys Ala Met Tyr Ala Pro Pro Ile Ser Gly 435 440 445 Gln Ile Arg Cys Ser Ser Asn Ile Thr Gly Leu Leu Leu Thr Arg Asp 450 455 460 Gly Gly Asn Ser Asn Asn Glu Ser Glu Ile Phe Arg Pro Gly Gly Gly 465 470 475 480 Asp Met Arg Asp Asn Trp Arg Ser Glu Leu Tyr Lys Tyr Lys Val Val 485 490 495 Lys Ile Glu Pro Leu Gly Val Ala Pro Thr Lys Ala Lys Arg Arg Val 500 505 510 Val Gln Arg Glu Lys Arg Ala Val Gly Ile Gly Ala Leu Phe Leu Gly 515 520 525 Phe Leu Gly Ala Ala Gly Ser Thr Met Gly Ala Ala Ser Met Thr Leu 530 535 540 Thr Val Gln Ala Arg Gln Leu Leu Ser Gly Ile Val Gln Gln Gln Asn 545 550 555 560 Asn Leu Leu Arg Ala Ile Glu Ala Gln Gln His Leu Leu Gln Leu Thr 565 570 575 Val Trp Gly Ile Lys Gln Leu Gln Ala Arg Ile Leu Ala Val Glu Arg 580 585 590 Tyr Leu Lys Asp Gln Gln Leu Leu Gly Ile Trp Gly Cys Ser Gly Lys 595 600 605 Leu Ile Cys Thr Thr Ala Val Pro Trp Asn Ala Ser Trp Ser Asn Lys 610 615 620 Ser Leu Glu Gln Ile Trp Asn Asn Met Thr Trp Met Glu Trp Asp Arg 625 630 635 640 Glu Ile Asn Asn Tyr Thr Ser Leu Ile His Ser Leu Ile Glu Glu Ser 645 650 655 Gln Asn Gln Gln Glu Lys Asn Glu Gln Glu Leu Leu Glu Leu Asp Lys 660 665 670 Trp Ala Ser Leu Trp Asn Trp Phe Asn Ile Thr Asn Trp Leu Trp Tyr 675 680 685 Ile Lys Leu Phe Ile Met Ile Val Gly Gly Leu Val Gly Leu Arg Ile 690 695 700 Val Phe Ala Val Leu Ser Val Val Asn Arg Val Arg Gln Gly Tyr Ser 705 710 715 720 Pro Leu Ser Phe Gln Thr His Leu Pro Ile Pro Arg Gly Pro Asp Arg 725 730 735 Pro Glu Gly Ile Glu Glu Glu Gly Gly Glu Arg Asp Arg Asp Arg Ser 740 745 750 Ile Arg Leu Val Asn Gly Ser Leu Ala Leu Ile Trp Asp Asp Leu Arg 755 760 765 Ser Leu Cys Leu Phe Ser Tyr His Arg Leu Arg Asp Leu Leu Leu Ile 770 775 780 Val Thr Arg Ile Val Glu Leu Leu Gly Arg Arg Gly Trp Glu Ala Leu 785 790 795 800 Lys Tyr Trp Trp Asn Leu Leu Gln Tyr Trp Ser Gln Glu Leu Lys Asn 805 810 815 Ser Ala Val Ser Leu Leu Asn Ala Thr Ala Ile Ala Val Ala Glu Gly 820 825 830 Thr Asp Arg Val Ile Glu Val Val Gln Gly Ala Tyr Arg Ala Ile Arg 835 840 845 His Ile Pro Arg Arg Ile Arg Gln Gly Leu Glu Arg Ile Leu Leu 850 855 860

Claims

1. Immunoreactive HTLV-III polypeptide expressed by cells transformed with a recombinant vector containing HTLV-III cDNA.

2. A polypeptide of claim 1 wherein said HTLV-III cDNA encodes an env gene sequence.

3. A polypeptide of claim 2 which is immunoreactive with sera of patients with acquired immunodeficiency syndrome or sera containing antibodies to HTLV-III.

4. A polypeptide of claim 1 wherein said HTLV-III cDNA encodes an env-lor gene sequence.

5. A polypeptide of claim 4 which is immunoreactive with sera of patients with acquired immunodeficiency syndrome or sera containing antibodies to HTLV-III.

6. A polypeptide of claim 1 wherein said HTLV-III cDNA is an EcoRI restriction fragment.

7. A polypeptide of claim 6 which is immunoreactive with sera of patients with acquired immunodeficiency syndrome or sera containing antibodies to HTLV-III.

8. Isolated HTLV-III envelope polypeptide.

9. Isolated HTLV-III polypeptide encoded by an env-lor gene sequence.

10. Isolated cDNA encoding an HTLV-III gene.

11. cDNA of claim 10 encoding the HTLV-III env gene.

12. cDNA of claim 10 encoding the HTLV-III env-lor gene sequence.

13. cDNA of claim 10 encoding an EcoRI restriction fragment of HITLV-III cDNA which encodes a polypeptide immunoreactive with sera of patients with acquired immunodeficiency syndrome or sera containing antibodies to HTLV-III.

14. Isolated cDNA encoding for an HTLV-III polypeptide which is immunoreactive.

15. Isolated cDNA of claim 14 encoding for an envelope polypeptide which is immunoreactive with sera of patients with acquired immunodeficiency syndrome or sera containing antibodies to HTLV-III.

16. Isolated cDNA of claim 14 which is an EcoRI restriction fragment.

17. A DNA probe comprising a DNA sequence which is essentially homologous to a portion of the HTLV-III genome unique to the virus.

18. A DNA probe of claim 17 wherein the DNA sequence is essentially homologous to a portion of the HTLV III genome which encodes a polypeptide immunoreactive with sera of AIDS patents.

19. A hybrid protein comprising an HTLV-III polypeptide linked to at least one other polypeptide.

20. A hybrid protein of claim 19 comprising an HTLV-III polypeptide linked to an indicator polypeptide.

21. A hybrid protein of claim 20 wherein said indicator polypeptide comprises beta-galactosidase.

22. An isolated RNA transcript of the env gene of HTLV-III.

23. An isolated RNA transcript of claim 22 having a label which emits a detectable signal.

24. An isolated RNA transcript of claim 23 wherein said label comprises a radioisotope.

25. A recombinant vector containing HTLV-III DNA capable of expression upon insertion into host cells.

26. OmpA vector containing HTLV-III cDNA.

27. pMR 100 vector containing HTLV-III cDNA.

28. A method of producing HTLV-III polypeptide, comprising the steps of: a. cleaving HTLV-III cDNA to produce cDNA fragments; b. inserting the cDNA fragments into an expression vector to form a recombinant vector; c. transforming an appropriate host cell with the recombinant vector; and d. culturing the transformed host cell under conditions sufficient for expression of the polypeptide encoded for by the inserted HTLV-III cDNA.

29. A method of claim 28 wherein the cleaving step comprises digesting the HTLV-III cDNA with restriction endonucleases to produce restriction fragments of cDNA.

30. A method of claim 28 wherein the cleaving step comprises shearing the HTLV-III cDNA to produce cDNA fragments.

31. A method of producing HTLV-III envelope polypeptide, comprising the steps of: a. cleaving HTLV-III genomic cDNA with the restriction endonuclease Sstl; b. digesting the cleaved cDNA with restriction endonucleases sufficient to generate restriction fragments which encompass at least a portion of the env gene; c. isolating the restriction fragments; d. producing DNA fragments of about 200-500 base pairs in length from the restriction fragments; e. isolating the DNA fragments of about 200-500 base pairs; f. inserting the isolated fragments into the open reading frame expression vector pMR100 for production of hybrid proteins comprising an env gene product and beta-galactosidase; g. transforming lac z E. coli cells with the vector; h. plating the transformed cells on MacConkey agar plates, maintaining the plates under conditions sufficient for the formation of colonies and selecting cell colonies exhibiting a red color; i. culturing transformed cells from the selected colonies under conditions which allow expression of the hybrid protein; j. obtaining cellular protein from the cultured transformed cells; k. separating the cellular protein obtained; l. contacting the separated protein with sera from AIDS patients to identify protein which is immunoreactive with the sera; and m. isolating the immunoreactive protein.

32. A fusion protein produced by the method of claim 31.

33. A method of claim 31, further comprising the step of separating the env gene expression product from the remainder of the hybrid protein.

34. A HTLV-III envelope polypeptide produced by the method of claim 33.

35. Antibody specifically reactive with HTLV-III envelope polypeptide.

36. An antibody of claim 35 which is monoclonal.

37. Anibody specifically reactive with HTLV-III polypeptide produced by recombinant DNA techniques.

38. An antibody of claim 37 which is monoclonal.

39. An immunoassay for the detection of HTLV-III employing antibody which reacts specifically with HTLV-III polypeptide produced by recombinant DNA techniques.

40. An immunoassay for the detection of HTLV-III employing antibody which reacts specifically with HTLV-III envelope polypeptide.

41. An immunoassay of claim 40 wherein said antibody is monoclonal.

42. A sandwich type immunoradiometric assay for the detection of HTLC III employing an immobilized antibody which reacts with HTLV-III polypeptide and a soluble antibody which reacts with HTLV-III polypeptide.

43. An assay kit comprising an antibody which reacts specifically with HTLV-III polypeptide bound to a solid phase and a labeled soluble antibody which reacts specifically with HTLV-III polypeptide.

44. A method of detecting antibodies against HTLV-III in a bodily fluid comprising the steps of: a. contacting an immunoadsorbent comprising an HTLV-III polypeptide bound to a solid phase with a bodily fluid until antibodies against HTLV-III polypeptide in the bodily fluid bind the solid phase polypeptide; b. separating the immunoadsorbent from the bodily fluid; c. contacting the immunoadsorbent with a labeled HTLV-III polypeptide or labeled antibody against human immunoglobulin; and d. determining the amount of labeled polypeptide bound to immunoadsorbent as an indication of antibody to HTLV-III.

45. A kit for determining the presence of antibody against HTLV-III in a bodily fluid comprising: a. an immunoadsorbent comprising a HTLV-III polypeptide bound to a solid phase; and b. labeled HLTV-III polypeptide or a labeled antibody against human immunoglobulin.

46. A method of detecting HTLV-III nucleic acid in a bodily fluid comprising the steps of: a. adsorbing the nucleic acid in a bodily fluid onto an adsorbent; b. denaturing the adsorbed nucleic acid; c. contacting the adsorbed nucleic acid with a HTLV-III DNA or RNA probe; and d. determining if the probe hybridizes with the adsorbed nucleic acid.

47. A method of claim 46 wherein the bodily fluid is a cell lysate.

48. A hybridoma cell line which produces antibody specifically reactive with HTLV-III envelope polypeptide.