Methods, kits, and probes for diagnosing HIV-2

Abstract

A method for diagnosing an HIV-2 (LAV-II) infection and a kit containing reagents for the same is disclosed. These reagents include cDNA probes which are capable of hybridizing to at least a portion of the genome of HIV-2. In one embodiment, the DNA probes are capable of hybridizing to the entire genome of HIV-2. These reagents also include polypeptides encoded by some of these DNA sequences.

Description

BACKGROUND OF THE INVENTION

The invention relates to cloned DNA sequences analogous to the genomic RNA of a virus known as Lymphadenopathy-Associated Virus II ("LAV-II"), a process for the preparation of these cloned DNA sequences, and their use as probes in diagnostic kits. In one embodiment, the invention relates to a cloned DNA sequence analogous to the entire genomic RNA of HIV-2 and its use as a probe. The invention also relates to polypeptides with amino acid sequences encoded by these cloned DNA sequences and the use of these polypeptides in diagnostic kits.

According to recently adopted nomenclature, as reported in Nature, May 1986, a substantially-identical group of retroviruses which has been identified as one causative agent of AIDS are now referred to as Human Immunodeficiency Viruses I (HIV-1). This previously-described group of retroviruses includes Lymphadenopathy-Associated Virus I (LAV-I), Human T-cell Lymphotropic Virus-III (HTLV-III), and AIDS-Related Virus (ARV).

Lymphadenopathy-Associated Virus II has been described in U.S. application Ser. No. 06/835,228, which was filed Mar. 3, 1986, now U.S. Pat. No. 4,939,288 and is specifically incorporated herein by reference Because LAV-II is a second, distinct causative agent of AIDS, LAV-II properly is classifiable as a Human Immunodeficiency Virus II (HIV-2). Therefore, "LAV-II" as used hereinafter describes a particular genus of HIV-2 isolates.

While HIV-2 is related to HIV-1 by its morphology, its tropism and its in vitro cytopathic effect on CD4 (T4) positive cell lines and lymphocytes, HIV-2 differs from previously described human retroviruses known to be responsible for AIDS. Moreover, the proteins of HIV-1 and 2 have different sizes and their serological cross-reactivity is restricted mostly to the major core protein, as the envelope glycoproteins of HIV-2 are not immune precipitated by HIV-1-positive sera except in some cases where very faint cross-reactivity can be detected. Since a significant proportion of the HIV infected patients lack antibodies to the major core protein of their infecting virus, it is important to include antigens to both HIV-1 and HIV-2 in an effective serum test for the diagnosis of the infection by these viruses.

HIV-2 was first discovered in the course of serological research on patients native to Guinea-Bissau who exhibited clinical and immunological symptoms of AIDS and from whom sero-negative or weakly sero-positive reactions to tests using an HIV-1 lysate were obtained. Further clinical studies on these patients isolated viruses which were subsequently named "LAV-II."

One LAV-II isolate, subsequently referred to as LAV-II MIR, was deposited at the Collection Nationale des Cultures de Micro-Organismes (CNCM) at the Institut Pasteur in Paris, France on Dec. 19, 1985 under Accession No. I-502 and has also been deposited at the British ECA CC under No. 87.001.001 on Jan. 9, 1987. A second LAV-II isolate was deposited at CNCM on Feb. 21, 1986 under Accession No. I-532 and has also been deposited at the British ECA CC under No. 87.001.002 on Jan. 9, 1987. This second isolate has been subsequently referred to as LAV-II ROD. Other isolates deposited at the CNCM on Dec. 19, 1986 are HIV-2 IRMO (No. I-642) and HIV-2 EHO (No. I-643). Several additional isolates have been obtained from West African patients, some of whom have AIDS, others with AIDS-related conditions and others with no AIDS symptoms. All of these viruses have been isolated on normal human lymphocyte cultures and some of them were thereafter propagated on lymphoid tumor cell lines such as CEM and MOLT.

Due to the sero-negative or weak sero-positive results obtained when using kits designed to identify HIV-1 infections in the diagnosis of these new patients with HIV-2 disease, it has been necessary to devise a new diagnostic kit capable of detecting HIV-2 infection, either by itself or in combination with an HIV-1 infection. The present inventors have, through the development of cloned DNA sequences analogous to at least a portion of the genomic RNA of LAV-II ROD viruses, created the materials necessary for the development of such kits.

SUMMARY OF THE INVENTION

As noted previously, the present invention relates to the cloned nucleotide sequences homologous or identical to at least a portion of the genomic RNA of HIV-2 viruses and to polypeptides encoded by the same. The present invention also relates to kits capable of diagnosing an HIV-2 infection.

Thus, a main object of the present invention is to provide a kit capable of diagnosing an infection caused by the HIV-2 virus. This kit may operate by detecting at least a portion of the RNA genome of the HIV-2 virus or the provirus present in the infected cells through hybridization with a DNA probe or it may operate through the immunodiagnostic detection of polypeptides unique to the HIV-2 virus.

Additional objects and advantages of the present invention will be set forth in part in the description which follows, or may be learned from practice of the invention. The objects and advantages may be realized and attained by means of the instrumentalities and combinations particularly pointed out in the appended claims.

To achieve these objects and in accordance with the purposes of the present invention, cloned DNA sequences related to the entire genomic RNA of the LAV-II virus are set forth. These sequences are analogous specifically to the entire genome of the LAV-II ROD strain.

To further achieve the objects and in accordance with the purposes of the present invention, a kit capable of diagnosing an HIV-2 infection is described. This kit, in one embodiment, contains the cloned DNA sequences of this invention which are capable of hybridizing to viral RNA or analogous DNA sequences to indicate the presence of an HIV-2 infection. Different diagnostic techniques can be used which include, but are not limited to: (1) Southern blot procedures to identify cellular DNA which may or may not be digested with restriction enzymes; (2) Northern blot techniques to identify RNA extracted from cells; and (3) dot blot techniques, i.e., direct filtration of the sample through an ad hoc membrane such as nitrocellulose or nylon without previous separation on agarose gel. Suitable material for dot blot technique could be obtained from body fluids including, but not limited to, serum and plasma, supernatants from culture cells, or cytoplasmic extracts obtained after cell lysis and removal of membranes and nuclei of the cells by centrifugation as accomplished in the "CYTODOT" procedure as described in a booklet published by Schleicher and Schull.

In an alternate embodiment, the kit contains the polypeptides created using these cloned DNA sequences. These polypeptides are capable of reacting with antibodies to the HIV-2 virus present in sera of infected individuals, thus yielding an immunodiagnostic complex.

It is understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention as claimed. The accompanying drawings, which are incorporated in and constitute a part of the specification, illustrate one embodiment of the invention and, together with the description, serve to explain the principles of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1B generally depict the nucleotide sequence of a cloned complementary DNA (cDNA) to the genomic RNA of HIV-2. FIG. 1A depicts the genetic organization of HIV-1, position of the HIV-1 HindIII fragment used as a probe to screen the cDNA library, and restriction map of the HIV-2 cDNA clone, E2. FIG. 1B depicts the nucleotide sequence of the 3' end of the 3' LTR of HIV-2. The corresponding region of the HIV-1 LTR was aligned using the Wilbur and Lipman algorithm (window: 10; K-tuple: 7; gap penalty: 3) as described by Wilbur and Lipman in Proc. Natl. Acad. Sci. USA 80: 726-730 (1983), specifically incorporated herein by reference. The U3-R junction in HIV-1 is indicated and the poly A addition signal and potential TATA promoter regions are boxed. In FIG. 1A, the symbols B, H, Ps and Pv refer to the restriction sites BamHI, HindIII, PstI and PvuII, respectively.

FIGS. 2A-2D generally depicts the HIV-2 specificity of the E2 clone. FIG. 2A and B are line drawing representing Southern Blots of DNA extracted from CEM cells infected with the following isolates: HIV-2.sub.ROD (a,c) HIV-2.sub.DUL (b,d) and HIV-1.sub.BRU (e,f). Blots a,b,f are PstI digested. Blots c,d,e are undigested. FIG. 2C and D are line drawings representing dot blot hybridization of pelleted virions from CEM cells infected by the HIV-1.sub.BRU (1), Simian Immunodeficiency Virus (SIV) isolate Mm 142-83 (3), HIV-2.sub.DUL (4), HIV-2.sub.ROD (5), and HIV-1.sub.ELI (6). Dot 2 is a pellet from an equivalent volume of supernatant from uninfected CEM. Thus, FIG. 2A and C depicts hybridization with the HIV-2 cDNA (E2) and FIG. 2B and D depicts hybridization to an HIV-1 probe consisting of a 9.2 kb SacI insert from HIV-1.sub.BRU.

FIGS. 3A-3B generally depict a restriction map of the HIV-2 ROD genome and its homology to HIV-1. FIG. 3A specifically depicts the organization of three recombinant phage lambda clones, ROD 4, ROD 27, and ROD 35. In FIG. 3A, the open boxes represent viral sequences, the LTR are filled, and the dotted boxes represent cellular flanking sequences (not mapped). Only some characteristic restriction enzyme sites are indicated. .lambda.ROD 27 and .lambda.35 are derived from integrated proviruses while .lambda.ROD 4 is derived from a circular viral DNA. The portion of the lambda clones that hybridizes to the cDNA E2 is indicated below the maps. A restriction map of the .lambda.ROD isolate was reconstructed from these three lambda clones. In this map, the restriction sites are identified as follows: B: BamHI; E: EcoRI; H: HindIII; K: KpnI; Ps: PstI; Pv: PvuII; S: SacI; X: XbaI. R and L are the right and left BamHI arms of the lambda L47.1 vector.

FIG. 3B specifically depicts dots 1-11 which correspond to the single-stranded DNA form of M13 subclones from the HIV-1.sub.BRU cloned genome. Their size and position on the HIV-1 genome, determined by sequencing is shown below the figure. Dot 12 is a control containing lambda phage DNA. The dot-blot was hybridized in low stringency conditions as described in Example 1 with the complete lambda .lambda.ROD 4 clone as a probe, and successively washed in 2.times.SSC, 0.1% SDS at 25.degree. C. (Tm-42.degree. C.), 1.times.SSC, 0.1% SDS at 60.degree. C. (Tm-20.degree. C.), and 0.1.times.SSC, 0.1% SDS at 60.degree. C. (Tm-3.degree. C.) and exposed overnight. A duplicate dot blot was hybridized and washed in stringent conditions (as described in Example 2) with the labelled lambda J19 clone carrying the complete HIV-1.sub.BRU genome. HIV-1 and HIV-2 probes were labelled the same specific activity (10.sup.8 cpm/g.).

FIGS. 4A-4B generally depict the restriction map polymorphism in different HIV-2 isolates and shows comparison of HIV-2 to SIV. FIG. 4A is a line drawing depicting DNA (20 .mu.g. per lane) from CEM cells infected by the isolate HIV-2.sub.DUL (panel 1) or peripheral blood lymphocytes (PBL) infected by the isolates HIV-2.sub.GOM (panel 2) and HIV-2.sub.MIR (panel 3) digested with: EcoRI (a), PstI (b), and HindIII (c). Much less viral DNA was obtained with HIV-2 isolates propagated on PBL. Hybridization and washing were in stringent conditions, as described in Example 2, with 10.sup.6 cpm/ml. of each of the E2 insert (cDNA) and the 5 kb. HindIII fragment of .lambda.ROD 4, labelled to 10.sup.9 cpm/.mu.g.

FIG. 4B is a line drawing depicting DNA from HUT 78 (a human T lymphoid cell line) cells infected with SIV Mm 142-83. The same amounts of DNA and enzymes were used as indicated in panel A. Hybridization was performed with the same probe as in A, but in non-stringent conditions. As described in Example 1 washing was for one hour in 2.times.SSC, 0.1% SDS at 40.degree. C. (panel 1) and after exposure, the same filter was re-washed in 0.1.times.SSC, 0.1% SDS at 60.degree. C. (panel 2). The autoradiographs were obtained after over-night exposition with intensifying screens.

FIG. 5 depicts plasmids .lambda.ROD 27, .lambda.ROD 35 and .lambda.ROD 4.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Reference will now be made in detail to the presently preferred embodiments of the invention, which, together with the following examples, serve to explain the principles of the invention.

The genetic structure of the HIV-2 virus has been analyzed by molecular cloning according to the method set forth herein and in the Examples. A restriction map of the genome of this virus is included in FIG. 4. In addition, the partial sequence of a cDNA complementary to the genomic RNA of the virus has been determined. This cDNA sequence information is included in FIG. 1.

Also contained herein is data describing the molecular cloning of the complete 9.5 kb genome of HIV-2, data describing the observation of restriction map polymorphism between different isolates, and an analysis of the relationship between HIV-2 and other human and simian retroviruses. From the totality of these data, diagnostic probes can be discerned and prepared.

Generally, to practice one embodiment of the present invention, a series of filter hybridizations of the HIV-2 RNA genome with probes derived from the complete cloned HIV-1 genome and from the gag and pol genes were conducted. These hybridizations yielded only extremely weak signals even in conditions of very low stringency of hybrization and washing. Thus, it was found to be difficult to assess the amount of HIV-2 viral and proviral DNA in infected cells by Southern blot techniques.

Therefore, a complementary DNA (cDNA) to the HIV-2 genomic RNA initially was cloned in order to provide a specific hybridization probe. To construct this cDNA, an oligo (dT) primed cDNA first-strand was made in a detergent-activated endogenous reaction using HIV-2 reverse transcriptase with virions purified from supernatants of infected CEM cells. The CEM cell line is a lymphoblastoid CD4+ cell line described by G. E. Foley et al. in Cancer 18: 522-529 (1965), specifically incorporated herein by reference. The CEM cells used were infected with the isolate ROD and were continuously producing high amounts of HIV-2.

After second-strand synthesis, the cDNAs were inserted into the TG130 M13 bacteria phage vector. A collection of 10.sup.4 M13 recombinant phages was obtained and screened in situ with an HIV-1 probe spanning 1.5 kb. of the 3' end of the LAV.sub.BRU isolate (depicted in FIG. 1A). Some 50 positive plaques were detected, purified, and characterized by end sequencing and cross-hybridizing the inserts. This procedure is described in more detail in Example 1 and in FIG. 1.

The different clones were found to be complementary to the 3' end of a polyadenylated RNA having the AATAAA signal about 20 nucleotides upstream of the poly A tail, as found in the long terminal repeat (LTR) of HIV-1. The LTR region of HIV-1 has been described by S. Wain Hobson et al. in Cell 40: 9-17 (1985), specifically incorporated herein by reference. The portion of the HIV-2 LTR that was sequenced was related only distantly to the homologous domain in HIV-1 as demonstrated in FIG. 1B. Indeed, only about 50% of the nucleotides could be aligned and about a hundred insertions/deletions need to be introduced. In comparison, the homology of the corresponding domains in HIV-1 isolates from USA and Africa is greater than 95% and no insertions or deletions are seen.

The largest insert of this group of M13 clones was a 2 kb. clone designated E2. Clone E2 was used as a probe to demonstrate its HIV-2 specificity in a series of filter hybridization experiments. Firstly, this probe could detect the genomic RNA of HIV-2 but not HIV-1 in stringent conditions as shown in FIG. 2, C and D. Secondly, positive signals were detected in Southern blots of DNA from cells infected with the ROD isolate as well as other isolates of HIV-2 as shown in FIG. 2, A and FIG. 4, A. No signal was detected with DNA from uninfected cells or HIV-1 infected cells, confirming the exogenous nature of HIV-2. In undigested DNA from HIV-2 infected cells, an approximately 10 kb. species, probably corresponding to linear unintegrated viral DNA, was principally detected along with a species with an apparent size of 6 kb., likely to be the circular form of the viral DNA. Conversely, rehybridization of the same filter with an HIV-1 probe under stringent conditions showed hybridization to HIV-1 infected cells only as depicted in FIG. 2, B.

To isolate the remainder of the genome of HIV-2, a genomic library in lambda phage L47.1 was constructed. Lambda phage L47.1 has been described by W. A. M. Loenen et al. in Gene 10: 249-259 (1980), specifically incorporated herein by reference. The genomic library was constructed with a partial Sau3AI restriction digest of the DNA from the CEM cell line infected with HIV-2.sub.ROD.

About 2.times.10.sup.6 recombinant plaques were screened in situ with labelled insert from the E2 cDNA clone. Ten recombinant phages were detected and plaque purified. Of these phages, three were characterized by restriction mapping and Southern blot hybridization with the E2 insert and probes from its 3' end (LTR) or 5' end (envelope), as well as with HIV-1 subgenomic probes. In this instance, HIV-1 probes were used under non-stringent conditions.

A clone carrying a 9.5 kb. insert and derived from a circular viral DNA was identified as containing the complete genome and designated .lambda.ROD 4. Two other clones, .lambda.ROD 27 and .lambda.ROD 35 were derived from integrated proviruses and found to carry an LTR and cellular flanking sequences and a portion of the viral coding sequences as shown in FIG. 3, A.

Fragments of the lambda clones were subcloned into a plasmid vector p UC 18.

Plasmid pROD 27-5' is derived from .lambda.ROD 27 and contains the 5' 2 Kb of the HIV-2 genome and cellular flanking sequences (5' LTR and 5' viral coding sequences to the EcoRI site)

Plasmid pROD 4.8 is derived from .lambda.ROD 4 and contains the about 5 kb HindIII fragments that is the central part of the HIV-2 genome.

Plasmid pROD 27-5' and pROD 4.8 inserts overlap.

Plasmid pROD 4.7 contains a HindIII 1.8 Kb fragment from .lambda.ROD 4. This fragment is located 3' to the fragment subcloned into pROD 4.8 and contains about 0.8 Kb of viral coding sequences and the part of the lambda phage (.lambda.L47.1) left arm located between the BamHI and HindIII cloning sites.

Plasmid pROD 35 contains all the HIV-2 coding sequences 3' to the EcoRI site, the 3' LTR and about 4 Kb of cellular flanking sequences.

Plasmid pROD 27-5' and pROD 35 in E. coli strain HB 101 are deposited respectively under No. 1-626 and 1-633 at the CNCM, and have also been deposited at the NCIB (British Collection). These plasmids are depicted in FIG. 5. Plasmid pROD 4.7 and pROD 4.8 in E. coli strain TG1 are deposited respectively under No. 1-627 and 1-628 at the CNCM.

To reconstitute the complete HIV-2 ROD genome, pROD 35 is linearized with EcoRI and the EcoRI insert of pROD 27-5' is ligated in the correct orientation into this site.

The relationship of HIV-2 to other human and simian retroviruses was surmised from hybridization experiments. The relative homology of the different regions of the HIV-1 and 2 genomes was determined by hybridization of fragments of the cloned HIV-1 genome with the labelled .lambda.ROD 4 expected to contain the complete HIV-2 genome (FIG. 3, B). Even in very low stringency conditions (Tm-42.degree. C.), the hybridization of HIV-1 and 2 was restricted to a fraction of their genomes, principally the gag gene (dots 1 and 2), the reverse transcriptase domain in pol (dot 3), the end of pol and the Q (or sor) genes (dot 5) and the F gene (or 3' orf) and 3' LTR (dot 11). The HIV-1 fragment used to detect the HIV-2 cDNA clones contained the dot 11 subclone, which hybridized well to HIV-2 under non-stringent conditions. Only the signal from dot 5 persisted after stringent washing. The envelope gene, the region of the tat gene and a part of pol thus seemed very divergent. These data, along with the LTR sequence obtained (FIG. 1, B), indicated that HIV-2 is not an envelope variant of HIV-1 as described by Alizon et al., Cell 40:63-74 (1986).

It was observed that HIV-2 is related more closely to the Simian Immunodeficiency Virus (SIV) than it is to HIV-1. This correlation has been described by F. Clavel et al. in C.R. Acad. Sci. (Paris) 302: 485-488 (1986) and F. Clavel et al. in Science 233: 343-346 (1986), both of which are specifically incorporated herein by reference. Simian Immunodeficiency Virus (also designated Simian T-cell Lymphotropic Virus Type 3, STLV-3) is a retrovirus first isolated from captive macaques with an AIDS-like disease in the USA. This simian virus has been described by M. D. Daniel et al. in Science 228: 1201-1204 (1985), specifically incorporated herein by reference.

All the SIV proteins, including the envelope, are immune precipitated by sera from HIV-2 infected patients, whereas the serological cross-reactivity of HIV-1 to 2 is restricted to the core proteins. However SIV and HIV-2 can be distinguished by slight differences in the apparent molecular weight of their proteins.

In terms of nucleotide sequence, it also appears that HIV-2 is closely related to SIV. The genomic RNA of SIV can be detected in stringent conditions as shown in FIG. 2, C by HIV-2 probes corresponding to the LTR and 3' end of the genome (E2) or to the gag or pol genes. Under the same conditions, HIV-1 derived probes do not detect the SIV genome as shown in FIG. 2, D.

In Southern blots of DNA from SIV-infected cells, a restriction pattern clearly different from HIV-2.sub.ROD and other isolates is seen. All the bands persist after a stringent washing, even though the signal is considerably weakened, indicating a sequence homology throughout the genomes of HIV-2 and SIV. It has recently been shown that baboons and macaques could be infected experimentally by HIV-2, thereby providing an interesting animal model for the study of the HIV infection and its preventive therapy. Indeed, attempts to infect non-human primates with HIV-1 have been successful only in chimpanzees, which are not a convenient model.

From an initial survey of the restriction maps for certain of the HIV-2 isolates obtained according to the methods described herein, it is already apparent that HIV-2, like HIV-1, undergoes restriction site polymorphism. FIG. 4A depicts examples of such differences for three isolates, all different one from another and from the cloned HIV-2.sub.ROD. It is very likely that these differences at the nucleotide level are accompanied by variations in the amino-acid sequence of the viral proteins, as evidenced in the case of HIV-1 and described by M. Alizon et al. in Cell 46: 63-74 (1986), specifically incorporated herein by reference. It is also to be expected that the various isolates of HIV-2 will exhibit other minor amino acid heterogeneities. See, for example, Clavel et al., Nature 324 (18): 691-695 (1986), specifically incorporated herein by reference.

Further, the characterization of HIV-2 will also delineate the domain of the envelope glycoprotein that is responsible for the binding of the surface of the target cells and the subsequent internalization of the virus. This interaction was shown to be mediated by the CD4 molecule itself in the case of HIV-1 and similar studies tend to indicate that HIV-2 uses the same receptor. Thus, although there is wide divergence between the env genes of HIV-1 and 2, small homologous domains of the envelopes of the two HIV could represent a candidate receptor binding site. This site could constitute a target for use to raise a protective immune response against this group of retroviruses.

From the data discussed herein, certain nucleotide sequences have been identified which are capable of being used as probes in diagnostic methods to obtain the immunological reagents necessary to diagnose an HIV-2 infection. In particular, these sequences may be used as probes in hybridization reactions with the genetic material of infected patients to indicate whether the RNA of the HIV-2 virus is present in these patient's lymphocytes or whether an analogous DNA is present. In this embodiment, the test methods which may be utilized include Northern blots, Southern blots and dot blots. One particular nucleotide sequence which may be useful as a probe is the combination of the 5 kb. HindIII fragment of ROD 4 and the E2 cDNA used in FIG. 4.

In addition, the genetic sequences of the HIV-2 virus may be used to create the polypeptides encoded by these sequences. Specifically, these polypeptides may be created by expression of the cDNA obtained according to the teachings herein in hosts such as bacteria, yeast or animal cells. These polypeptides may be used in diagnostic tests such as immunofluorescence assays (IFA), radioimmunoassays (RIA) and Western Blot tests.

Moreover, it is also contemplated that additional diagnostic tests, including additional immunodiagnostic tests, may be developed in which the DNA probes or the polypeptides of this invention may serve as one of the diagnostic reagents. The invention described herein includes these additional test methods.

In addition, monoclonal antibodies to these polypeptides or fragments thereof may be created. The monoclonal antibodies may be used in immunodiagnostic tests in an analogous manner as the polypeptides described above.

The polypeptides of the present invention may also be used as immunogenic reagents to induce protection against infection by HIV-2 viruses. In this embodiment, the polypeptides produced by recombinant-DNA techniques would function as vaccine agents.

Also, the polypeptides of this invention may be used in competitive assays to test the ability of various antiviral agents to determine their ability to prevent the virus from fixing on its target.

Thus, it is to be understood that application of the teachings of the present invention to a specific problem or environment will be within the capabilities of one having ordinary skill in the art in light of the teachings contained herein. Examples of the products of the present invention and representative processes for their isolation and manufacture appear above and in the following examples.

EXAMPLES

Example 1

Cloning of a cDNA Complementary to Genomic RNA From HIV-2 Virions

HIV-2 virions were purified from 5 liters of supernatant from a culture of the CEM cell line infected with the ROD isolate and a cDNA first strand using oligo (dT) primer was synthesized in detergent activated endogenous reaction on pelleted virus, as described by M. Alizon et al. in Nature, 312: 757-760 (1984), specifically incorporated herein by reference. RNA-cDNA hybrids were purified by phenol-chloroform extraction and ethanol precipitation. The second-strand cDNA was created by the DNA polymerase I/RNAase H method of Sanger et al. described in Proc. Nat'l. Acad. Sci. USA, 74: 5463-5467 (1977), specifically incorporated herein by reference. The double-stranded cDNA was blunt-ended with T4 DNA polymerase using a commercial cDNA synthesis kit (obtained from Amersham). After attachment of EcoRI linkers (obtained from Pharmacia), EcoRI digestion, and ligation into EcoRI-digested dephosphorylated M13 tg 130 vector (obtained from Amersham), a cDNA library was obtained by transformation of the E. coli TG1 strain. Recombinant plaques (10.sup.4) were screened in situ on replica filters with the 1.5 kb. HindIII fragment from clone J19, corresponding to the 3' part of the genome of the LAV.sub.BRU isolate of HIV-1, .sup.32 P labelled to a specific activity of 10.sup.9 cpm .mu.g. The filters were prehybridized in 5.times.SSC, 5.times.Denhardt solution, 25% formamide, and denatured salmon sperm DNA (100 .mu.g/ml.) at 37.degree. C. for 4 hours and hybridized for 16 hours in the same buffer (Tm-42.degree. C.) plus 4.times.10.sup.7 cpm of the labelled probe (10.sup.6 cpm/ml. of hybridization buffer). The washing was done in 5.times.SSC, 0.1% SDS at 25.degree. C. for 2 hours. 20.times.SSC is 3M NaCl, 0.3M Na citrate. Positive plaques were purified and single-stranded M13 DNA prepared and end-sequenced according to the method of Sanger et al., supra.

Example 2

Hybridization of DNA from HIV-1 and HIV-2 Infected Cells and RNA from HIV-1 and 2 and SIV Virons With a Probe Derived From an HIV-2 Cloned cDNA

DNA was extracted from infected CEM cells continuously producing HIV-1 or 2. The DNA digested with 20 .mu.g of PstI or undigested, was electrophoresed on a 0.8% agarose gel, and Southern-transferred to nylon membrane. Virion dot-blots were prepared in duplicate, as described by F. Clavel et al. in Science 233: 343-346 (1986), specifically incorporated herein by reference, by pelleting volumes of supernatant corresponding to the same amount of reverse transcriptase activity. Prehybridization was done in 50% formamide, 5.times.SSC, 5.times.Denhardt solution, and 100 mg./ml. denatured salmon sperm DNA for 4 hours at 42.degree. C. Hybridization was performed in the same buffer plus 10% Dextran sulphate, and 10.sup.6 cpm/ml. of the labelled E2 insert (specific activity 10.sup.9 cpm/.mu.g.) for 16 hours at 42.degree. C. Washing was in 0.1.times.SSC, 0.1% SDS for 2.times.30 min. After exposure for 16 hours with intensifying screens, the Southern blot was dehybridized in 0.4N NaOH, neutralized, and rehybridized in the same conditions to the HIV-1 probe labelled to 10.sup.9 cpm/.mu.g.

Example 3

Cloning in Lambda Phage of the Complete Provirus DNA of HIV-2

DNA from the HIV-2.sub.ROD infected CEM (FIG. 2, lanes a and c) was partially digested with Sau3AI. The 9-15 kb. fraction was selected on a 5-40% sucrose gradient and ligated to BamHI arms of the lambda L47.1 vector. Plaques (2.times.10.sup.6) obtained after in vitro packaging and plating on E. coli LA 101 strain were screened in situ with the insert from the E2 cDNA clone. Approximately 10 positive clones were plaque purified and propagated on E. coli C600 recBC. The ROD 4, 27, and 35 clones were amplified and their DNA characterized by restriction mapping and Southern blotting with the HIV-2cDNA clone under stringent conditions, and gag-pol probes from HIV-1 used under non stringent conditions.

Example 4

Sequences of the Coding Regions for the Evelope Protein and GAG Product of the ROD HIV-2 Isolate

Additional experimental analysis of the HIV-2 ROD isolate was performed and has yielded the following sequences for the env and gag sequences. Regions coding for amino acid sequences corresponding to known proteins characterized by apparent molecular weights have been identified within the gag sequence: p. 16 (nucleotides 1-405), p. 26 (406-1155) and p. 12 (1156-1566). ##STR1##

Example 5

Peptide Sequences Encoded By The ENV and GAG Sequences

The following coding regions for antigenic peptides, identified by nucleotide numbers within the gene sequences of Example 4, are of particular interest. ##STR2##

Of the foregoing peptides,env1, env2, env3 and gag1 are particularly contemplated for diagnostic purposes, and env4, env5, env6, env7, env8, env9, env10 and env11 are particularly contemplated as protecting agents. The foregoing peptides can be synthesized by conventional protein synthesis techniques, such as that of Merrified.

It will be apparent to those skilled in the art that various modifications and variations can be made in the processes and products of the present invention. Thus, it is intended that the present application cover the modifications and variations of this invention provided they come within the scope of the appended claims and their equivalents.

Claims

1. A kit for determining the effectiveness of an antiviral agent in preventing an HIV-2 virus from binding to a target cell, comprising:

an antiviral agent;

one or more labeled peptides selected from the group consisting of:

(1) env1, comprising a peptide encoded by nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TITAG ACAAG TCTGC;

(2) env2, comprising a peptide encoded by nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising a peptide encoded by nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA;

(4) env4, comprising a peptide encoded by nucleotides 55-129 of the envelope sequence of HIV-2, having the following sequence:

TGCAC CCAAT ATGTA ACTGT TTTCT ATGGC GTACC CACGT GGAAA AATGC AACCA TTCCC CTGTT TTGTG CAACC;

(5) env5, comprising a peptide encoded by nucleotides 175-231 of the envelope sequence of HIV-2, having the following sequence:

GATGA TTATC AGGAA ATAAC TTTGA ATGTA ACAGA GGCTT TTGAT GCATG GAATA AT;

(6) env6, comprising a peptide encoded by nucleotides 274-330 of the envelope sequence of HIV-2, having the following sequence:

GAGAC ATCAA TAAAA CCATG TGTGA AACTA ACACC TTTAT GTGTA GCAAT GAAAT GC;

(7) env7, comprising a peptide encoded by nucleotides 607-660 of the envelope sequence of HIV-2, having the following sequence:

AACCA TTGCA ACACA TCAGT CATCA CAGAA TCATG TGACA AGCAC TATTG GGAT;

(8) env8, comprising a peptide encoded by nucleotides 661-720 of the envelope sequence of HIV-2, having the following sequence:

GCTAT AAGGT TTAGA TACTG TGCAC CACCG GGTTA TGCCC TATTA AGATG TAATG ATACC;

(9) env9, comprising a peptide encoded by nucleotides 997-1044 of the envelope sequence of HIV-2, having the following sequence:

AAAAG ACCCA GACAA GCATG GTGCT GGTTC AAAGG CAAAT GGAAA GAC;

(10) env10, comprising a peptide encoded by nucleotides 1132-1215 of the envelope sequence of HIV-2, having the following sequence:

AAAGG CTCAG ACCCA GAAGT AGCAT ACATG TGGAC TAACT GCAGA GGAGA GTTTC TCTAC TGCAA CATGA CTTGG TTCCT CAAT;

(11) env11, comprising a peptide encoded by nucleotides 1237-1305 of the envelope sequence of HIV-2, having the following sequence:

CGCAA TTATG CACCG TGCCA TATAA AGCAA ATAAT TAACA CATGG CATAA GGTAG GGAGA AATGT ATAT; and

(12) gag1, comprising a peptide encoded by nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC; and

a target cell.

2. An in vitro diagnostic method for the detection of the presence or absence of antibodies which bind to antigens of HIV-2 comprising:

(a) contacting a biological sample with one or more of the peptides selected from the group consisting of:

(1) env1, comprising a peptide encoded by nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TTTAG ACAAG TCTGC;

(2) env2, comprising a peptide encoded by nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising a peptide encoded by nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA;

(4) env4, comprising a peptide encoded by nucleotides 55-129 of the envelope sequence of HIV-2, having the following sequence:

TGCAC CCAAT ATGTA ACTGT TTTCT ATGGC GTACC CACGT GGAAA AATGC AACCA TTCCC CTGTT TTGTG CAACC;

(5) env5, comprising a peptide encoded by nucleotides 175-231 of the envelope sequence of HIV-2, having the following sequence:

GATGA TTATC AGGAA ATAAC TTTGA ATGTA ACAGA GGCTT TTGAT GCATG GAATA AT;

(6) env6, comprising a peptide encoded by nucleotides 274-330 of the envelope sequence of HIV-2, having the following sequence:

GAGAC ATCAA TAAAA CCATG TGTGA AACTA ACACC TTTAT GTGTA GCAAT GAAAT GC;

(7) env7, comprising a peptide encoded by nucleotides 607-660 of the envelope sequence of HIV-2, having the following sequence:

AACCA TTGCA ACACA TCAGT CATCA CAGAA TCATG TGACA AGCAC TATTG GGAT;

(8) env8, comprising a peptide encoded by nucleotides 661-720 of the envelope sequence of HIV-2, having the following sequence:

GCTAT AAGGT TTAGA TACTG TGCAC CACCG GGTTA TGCCC TATTA AGATG TAATG ATACC;

(9) env9, comprising a peptide encoded by nucleotides 997-1044 of the envelope sequence of HIV-2, having the following sequence:

AAAAG ACCCA GACAA GCATG GTGCT GGTTC AAAGG CAAAT GGAAA GAC;

(10) env10, comprising a peptide encoded by nucleotides 1132-1215 of the envelope sequence of HIV-2, having the following sequence:

AAAGG CTCAG ACCCA GAAGT AGCAT ACATG TGGAC TAACT GCAGA GGAGA GTTTC TCTAC TGCAA CATGA CTTGG TTCCT CAAT;

(11) env11, comprising a peptide encoded by nucleotides 1237-1305 of the envelope sequence of HIV-2, having the following sequence:

CGCAA TTATG CACCG TGCCA TATAA AGCAA ATAAT TAACA CATGG CATAA GGTAG GGAGA AATGT ATAT; and

(12) gag1, comprising a peptide encoded by nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC; and

(b) detecting the formation of an antigen-antibody complex between said one or more peptides and antibodies present in said biological sample.

3. The method of claim 2, wherein the formation of said antigen-antibody complex is detected by a process selected from the consisting of radioimmunoassay, immunosorbent assay, radioimmunoprecipitation assay, immunofluorescence assay, enzyme-linked assay, and Western blot.

4. The method of claim 2, wherein said peptide is labeled with a compound selected from the group consisting of radioisotopes, enzymes, fluorescent labels, chemiluminescent labels, and chromophores.

5. An in vitro diagnostic method for the detection of the presence or absence of antibodies which bind to antigens of a Human Immunodeficiency Virus Type 2 (HIV-2) comprising:

(a) contacting a biological sample with one or more peptides selected from the group consisting of:

(1) env1, comprising a peptide encoded by nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TTTAG ACAAG TCTGC;

(2) env2, comprising a peptide encoded by nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising a peptide encoded by nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA; and

(4) gag1, comprising a peptide encoded by nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC; and

(b) detecting the formation of an antigen-antibody complex between said one or more peptides and antibodies present in said biological sample.

6. The method of claim 5, wherein the formation of said antigen-antibody complex is detected by a process selected from the group consisting of radioimmunoassay, immunosorbent assay, radioimmunoprecipitation assay, immunofluorescence assay, enzyme-linked assay, and Western blot.

7. The method of claim 5, wherein the one or more peptides contained in the composition is labeled with a compound selected from the group consisting of radioisotopes, enzymes, fluorescent labels, chemiluminescent labels, and chromophores.

8. An in vitro diagnostic method for the detection of the presence or absence of nucleic acid which binds to nucleic acid of a Human Immunodeficiency Virus Type 2 (HIV-2) comprising:

(a) contacting a biological sample with one or more nucleic acid probes having a sequence selected from the group consisting of:

(1) env1, comprising nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TTTAG ACAAG TCTGC;

(2) env2, comprising nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA;

(4) env4, comprising nucleotides 55-129 of the envelope sequence of HIV-2, having the following sequence:

TGCAC CCAAT ATGTA ACTGT TTTCT ATGGC GTACC CACGT GGAAA AATGC AACCA TTCCC CTGTT TTGTG CAACC;

(5) env5, comprising nucleotides 175-231 of the envelope sequence of HIV-2, having the following sequence:

GATGA TTATC AGGAA ATAAC TTTGA ATGTA ACAGA GGCTT TTGAT GCATG GAATA AT;

(6) env6, comprising nucleotides 274-330 of the envelope sequence of HIV-2, having the following sequence:

GAGAC ATCAA TAAAA CCATG TGTGA AACTA ACACC TTTAT GTGTA GCAAT GAAAT GC;

(7) env7, comprising nucleotides 607-660 of the envelope sequence of HIV-2, having the following sequence:

AACCA TTGCA ACACA TCAGT CATCA CAGAA TCATG TGACA AGCAC TATTG GGAT;

(8) env8, comprising nucleotides 661-720 of the envelope sequence of HIV-2, having the following sequence:

GCTAT AAGGT TTAGA TACTG TGCAC CACCG GGTTA TGCCC TATTA AGATG TAATG ATACC;

(9) env9, comprising nucleotides 997-1044 of the envelope sequence of HIV-2, having the following sequence:

AAAAG ACCCA GACAA GCATG GTGCT GGTTC AAAGG CAAAT GGAAA GAC;

(10) env10, comprising nucleotides 1132-1215 of the envelope sequence of HIV-2, having the following sequence:

AAAGG CTCAG ACCCA GAAGT AGCAT ACATG TGGAC TAACT GCAGA GGAGA GTTTC TCTAC TGCAA CATGA CTTGG TTCCT CAAT;

(11) env11, comprising nucleotides 1237-1305 of the envelope sequence of HIV-2, having the following sequence:

CGCAA TTATG CACCG TGCCA TATAA AGCAA ATAAT TAACA CATGG CATAA GGTAG GGAGA AATGT ATAT; and

(12) gag1, comprising nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC; and

(b) detecting the formation of hybrids between said one or more nucleic acid probes and nucleic acid present in said biological sample.

9. The method of claim 8, wherein said nucleic acid is DNA.

10. The method of claim 8, wherein one or more nucleic acid probes are labeled with a compound selected from the group consisting of radioisotopes, enzymes, fluorescent labels, chemiluminescent labels, and chromophores.

11. An in vitro diagnostic method for the detection of the presence or absence of nucleic acid which binds to nucleic acid of a Human Immunodeficiency Virus Type 2 (HIV-2) comprising:

(a) contacting a biological sample with one or more nucleic acid probes having a sequence selected from the group consisting of:

(1) env1, comprising nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TTTAG ACAAG TCTGC;

(2) env2, comprising nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA; and

(4) gag1, comprising nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC; and

(b) detecting the formation of hybrids between said one or more nucleic acid probes and nucleic acid present in said biological sample.

12. The method of claim 11, wherein said nucleic acid is DNA.

13. The method of claim 11, wherein said one or more nucleic acid probes are labeled with a compound selected from the group consisting of radioisotopes, enzymes, fluorescent labels, chemiluminescent labels, and chromophores.

14. A method for determining the effectiveness of an antiviral agent in preventing an HIV-2 virus from binding to a target cell, comprising:

combining an antiviral agent to be tested with one or more labeled peptides selected from the group consisting of:

(1) env1, comprising a peptide encoded by nucleotides 1735-1809 of the envelope sequence of HIV-2, having the following sequence:

GTCAC TGCTA TAGAG AAGTA CCTAC AGGAC CAGGC GCGGC TAAAT TCATG GGGAT GTGCG TTTAG ACAAG TCTGC;

(2) env2, comprising a peptide encoded by nucleotides 1912-1983 of the envelope sequence of HIV-2, having the following sequence:

AGTAA AAGTT TAGAA CAGGC ACAAA TTCAG CAAGA GAAAA ATATG TATGA ACTAC AAAAA TTAAA TAGCT GG;

(3) env3, comprising a peptide encoded by nucleotides 1482-1530 of the envelope sequence of HIV-2, having the following sequence:

CCTAC AAAAG AAAAA AGATA CTCCT CTGCT CACGG GAGAC ATACA AGA;

(4) env4, comprising a peptide encoded by nucleotides 55-129 of the envelope sequence of HIV-2, having the following sequence:

TGCAC CCAAT ATGTA ACTGT TTTCT ATGGC GTACC CACGT GGAAA AATGC AACCA TTCCC CTGTT TTGTG CAACC;

(5) env5, comprising a peptide encoded by nucleotides 175-231 of the envelope sequence of HIV-2, having the following sequence:

GATGA TTATC AGGAA ATAAC TTTGA ATGTA ACAGA GGCTT TTGAT GCATG GAATA AT;

(6) env6, comprising a peptide encoded by nucleotides 274-330 of the envelope sequence of HIV-2, having the following sequence:

GAGAC ATCAA TAAAA CCATG TGTGA AACTA ACACC TTTAT GTGTA GCAAT GAAAT GC;

(7) env7, comprising a peptide encoded by nucleotides 607-660 of the envelope sequence of HIV-2, having the following sequence:

AACCA TTGCA ACACA TCAGT CATCA CAGAA TCATG TGACA AGCAC TATTG GGAT;

(8) env8, comprising a peptide encoded by nucleotides 661-720 of the envelope sequence of HIV-2, having the following sequence:

GCTAT AAGGT TTAGA TACTG TGCAC CACCG GGTTA TGCCC TATTA AGATG TAATG ATACC;

(9) env9, comprising a peptide encoded by nucleotides 997-1044 of the envelope sequence of HIV-2, having the following sequence:

AAAAG ACCCA GACAA GCATG GTGCT GGTTC AAAGG CAAAT GGAAA GAC;

(10) env10, comprising a peptide encoded by nucleotides 1132-1215 of the envelope sequence of HIV-2, having the following sequence:

AAAGG CTCAG ACCCA GAAGT AGCAT ACATG TGGAC TAACT GCAGA GGAGA GTTTC TCTAC TGCAA CATGA CTTGG TTCCT CAAT;

(11) env11, comprising a peptide encoded by nucleotides 1237-1305 of the envelope sequence of HIV-2, having the following sequence:

CGCAA TTATG CACCG TGCCA TATAA AGCAA ATAAT TAACA CATGG CATAA GGTAG GGAGA AATGT ATAT; and

(12) gag1, comprising a peptide encoded by nucleotides 991-1053 of the GAG sequence of HIV-2, having the following sequence:

GACTG TAAAT TAGTG CTAAA AGGAC TAGGG ATGAA CCCTA CCTTA GAAGA GATGC TGACC GCC;

adding said antiviral agent and said one or more peptides to a composition comprising a target cell;

determining the amount of labeled peptide-target cell binding of the composition comprising said antiviral agent;

determining the amount of labeled peptide-target cell binding of a control composition lacking said antiviral agent; and

determining the relative amount of labeled peptide-target cell binding of the composition comprising said antiviral agent compared to the amount of labeled peptide-target cell binding in the control composition lacking said antiviral agent,

wherein an antiviral agent having a low affinity for binding to the target cell is evidenced by little or no change between the binding values of the control composition and the composition comprising the antiviral agent, and an antiviral agent having a high affinity for binding to the target cell is evidenced by a lower binding value in the presence of the antiviral agent in comparison to the control composition lacking the antiviral agent.