# Patent

## Title
Cloned DNA sequence related to genomic RNA of human immunodeficiency virus (HIV-1)

## Abstract

This invention is in the field of lymphadenopathy virus, which has been designated Human Immunodeficiency Virus Type 1 (HIV-1). This invention relates to a diagnostic means and method to detect the presence of DNA, RNA or antibodies of the lymphadenopathy retrovirus associated with the acquired immune deficiency syndrome or of the lymphadenopathy syndrome by the use of DNA fragments or the peptides encoded by said DNA fragments. The invention further relates to the DNA fragments, vectors comprising them and the proteins expressed.

## Background
This application is a division of application Ser. No. 06/771,248, filed Aug. 30, 1985 (now abandoned). This application is also a continuation-in-part of application Ser. No. 07/999,410, filed Dec. 31, 1992 (pending), which is a continuation of application Ser. No. 07/499,210 filed Mar. 19, 1990 now abandoned, which is a continuation of application Ser. No. 06/771,230, filed Aug. 30, 1985 (now abandoned), which is a continuation-in-part of application Ser. No. 06/706,562, filed Feb. 28, 1985 (now abandoned), which is a continuation-in-part of application Ser. No. 06/558,109, filed Dec. 5, 1983 (now abandoned).


BACKGROUND OF THE INVENTION
This invention relates to cloned DNA sequences indistinguishable from genomic RNA and DNA of lymphadenopathy-associated virus (LAV), a process for their preparation and their uses. It relates more particularly to stable probes including a DNA sequence which can be used for the detection of the LAV virus or related viruses or DNA proviruses in any medium, particularly biological samples containing any of them. The invention also relates to polypeptides, whether glycosylated or not, encoded by said DNA sequences.
Lymphadenopathy-associated virus (LAV) is a human retrovirus first isolated from the lymph node of a homo-sexual patient with lymphadenopathy syndrome, frequently a prodrome or a benign form of acquired immune deficiency syndrome (AIDS). Subsequently, other LAV isolates were recovered from patients with AIDS or pre-AIDS. All available data are consistent with the virus being the causative agent of AIDS.
A method for cloning such DNA sequences has already been disclosed in British Patent Application Nr. 84 23659, filed on Sep. 19, 1984. Reference is hereafter made to that application as concerns subject matter in common with the further improvements to the invention disclosed herein.
SUMMARY OF THE INVENTION
The present invention aims at providing additional new means which are not only useful for the detection of LAV or related viruses, (hereafter more generally referred to as “LAV viruses” or “Human Immunodeficiency Virus Type 1” or simply “HIV-1”, but also new means that have more versatility, particularly in detecting specific parts of the genomic RNA of said viruses whose expression products are not always directly detectable by immunological methods.
The present invention further aims at providing polypeptides containing sequences in common with polypeptides encoded by the LAV genomic RNA. It relates even more particularly to polypeptides comprising antigenic determinants included in the proteins encoded and expressed by the LAV genome occurring in nature. An additional object of the invention is to further provide means for the detection of proteins related to LAV virus, particularly for the diagnosis of AIDS or pre-AIDS or, to the contrary, for the detection of antibodies against the LAV virus or proteins related therewith, particularly in patients afflicted with AIDS or pre-AIDS or more generally in asymptomatic carriers and in blood-related products. Finally, the invention also aims at providing immunogenic polypeptides, and more particularly protective polypeptides for use in the preparation of vaccine compositions against AIDS or related syndromes.
The present invention relates to additional DNA fragments, hybridizable with the genomic RNA of LAV as they will be disclosed hereafter, as well as with additional cDNA variants corresponding to the whole genomes of LAV viruses. It further relates to DNA recombinants containing said DNAs or cDNA fragments.
The invention relates more particularly to a cDNA variant corresponding to the whole of LAV retroviral genomes, which is characterized by a series of restriction sites in the order hereafter (from the 5′ end to the 3′ end).
The coordinates of the successive sites of the whole LAV genome (restriction map) are indicated hereafter too, with respect to the Hind III site (selected as of coordinate 1) which is located in the R region. The coordinates are estimated with an accuracy of ±200 bp:

















Hind III
0




Sac I
50



Hind III
520



Pst I
800



Hind III
1 100



Bgl II
1 500



Kpn I
3 500



Kpn I
3 900



Eco RI
4 100



Eco RI
5 300



Sal I
5 500



Kpn I
6 100



Bgl II
6 500



Bgl II
7 600



Hind III
7 850



Bam HI
8 150



Xho I
8 600



Kpn I
8 700



Bgl II
8 750



Bgl II
9 150



Sac I
9 200



Hind III
9 250










Another DNA variant according to this invention optionally contains an additional Hind III approximately at the 5 550 coordinate.
Reference is further made to FIG. 1 which shows a more detailed restriction map of said whole DNA (λJ19).
An even more detailed nucleotide sequence of a preferred DNA according to the invention is shown in FIGS. 4–12 hereafter.
The invention further relates to other preferred DNA fragments which will be referred to hereafter.



BRIEF DESCRIPTION OF THE DRAWINGS
Additional features of the invention will appear in the course of the non-limitative disclosure of additional features of preferred DNAs of the invention, as well as of preferred polypeptides according to the invention. Reference will further be had to the drawings in which:
FIG. 1 is the restriction map of a complete LAV genome (clone λJ19);
FIGS. 2 and 3 show diagrammatically parts of the three possible reading phases of LAV genomic RNA, including the open reading frames (ORF) apparent in each of said reading phases;
FIGS. 4–12 show the successive nucleotide sequences of a complete LAV genome. The possible peptide sequences in relation to the three possible reading phases related to the nucleotide sequences shown are also indicated;
FIGS. 13–18 reiterate the sequence of part of the LAV genome containing the genes coding for the envelope proteins, with particular boxed peptide sequences which correspond to groups which normally carry glycosyl groups.
FIGS. 19–26 reiterate the DNA sequence of the LAV genome.



DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
The sequencing and determination of sites of particular interest were carried out on a phage recombinant corresponding to λJ19 disclosed in the abovesaid British Patent application Nr. 84 23659. A method for preparing it is disclosed in that application.
The whole recombinant phage DNA of clone λJ19 (disclosed in the earlier application) was sonicated according to the protocol of DEININGER (1983). Analytical Biochem. 129, 216. The was repaired by a Klenow reaction for 12 hours at 16° C. The DNA was electrophoresed through 0.8% agarose gel and DNA in the size range of 300–600 bp was cut out and electroeluted and precipitated. Resuspended DNA (in 10 mM Tris, pH 8; 0, 1 mM EDTA) was ligated into M13mp8 RF DNA (cut by the restriction enzyme SmaI and subsequently alkaline phosphated), using T4 DNA- and RNA-ligases (Maniatis et al (1982)—Molecular cloning—Cold Spring Harbor Laboratory). An E. coli strain designated as TG1 was used for further study. This strain has the following genotype:
Δlac pro, supE, thi.F′traD36, proAB, lacIq, ZΔM15, r−
This E. coli TGI strain has the peculiarity of enabling recombinants to be recognized easily. The blue colour of the cells transfected with plasmids which did not recombine with a fragment of LAV DNA is not modified. To the contrary cells transfected by a recombinant plasmid containing a LAV DNA fragment yield white colonies. The technique which was used is disclosed in Gene (1983), 26, 101.
This strain was transformed with the ligation mix using the Hanahan method (Hanahan D (1983) J. Mol. Biol. 166, 557). Cells were plated out on tryptone-agarose plate with IPTG and X-gal in soft agarose. White plaques were either picked and screened or screened directly in situ using nitrocellulose filters. Their DNAs were hybridized with nick-translated DNA inserts of pUC18 Hind III subclones of λJ19. This permitted the isolation of the plasmids or subclones of λ which are identified in the table hereafter. In relation to this table it should also be noted that the designation of each plasmid is followed by the deposition number of a cell culture of E. coli TGI containing the corresponding plasmid at the “Collection Nationale des Cultures de Micro-organismes” (C.N.C.M.) of the Pasteur Institute in Paris, France. A non-transformed TGI cell line was also deposited at the C.N.C.M. under Nr. I-364. All these deposits took place on Nov. 15, 1984. The sizes of the corresponding inserts derived from the LAV genome have also been indicated.







TABLE





Essential features of the recombinant plasmids



















pJ19-1 plasmid
(I-365)
0.5 kb



Hind III - Sac I - Hind III



pJ19-17 plasmid
(I-367)
0.6 kb



Hind III - Pst 1 - Hind III



pJ19-6 plasmid
(I-366)
1.5 kb



Hind III (5′)



Bam HI



Xho I



Kpn I



Bgl II



Sac I (3′)



Hind III



pJ19-13 plasmid
(I-368)
6.7 kb



Hind III (5′)



Bgl II



Kpn I



Kpn I



Eco RI



Eco RI



Sal I



Kpn I



Bgl II



Bgl II



Hind III (3′)










Positively hybridizing M13 phage plates were grown up for 5 hours and the single-stranded DNAs were extracted.
M13mp8 subclones of λJ19 DNAs were sequenced according to the dideoxy method and technology devised by Sanger et al Sanger (1977), Proc. Natl. Acad. Sci. USA, 74, 5463 and M13 cloning and sequencing handbook, AMERSHAM (1983). The 17-mer oligonucleotide primer α-35SdATP (400 Ci/mmol, AMERSHAM), and 0.5×–5× buffer gradient gels (Biggen M. D. et al (1983), Proc. Natl. Acad. Sci. USA 50, 3963) were used. Gels were read and put into the computer under the programs of Staden (Staden R. (1982), Nucl. Acids Res. 10, 4731). All the appropriate references and methods can be found in the AMERSHAM M13 cloning and sequencing handbook.
The complete sequence of λJ19 was deduced from the experiments as further disclosed hereafter.
FIGS. 4–12 provide the DNA nucleotide sequence of the complete genome of LAV. The numbering of the nucleotides starts from a left most Hind III restriction site (5′AAG . . . ) of the restriction map. The numbering occurs in tens whereby the last zero number of each of the numbers occurring on the drawings is located just below the nucleotide corresponding to the nucleotides designated. That is the nucleotide at position 10 is T, the nucleotide at position 20 is C, etc.
Above each of the lines of the successive nucleotide sequences there are provided three lines of single letters corresponding to the amino acid sequence deduced from the DNA sequence (using the genetic code) for each of the three reading phases, whereby said single letters have the following meanings.
A: alanine
R: arginine
K: lysine
H: histidine
C: cysteine
M: méthionine
W: tryptophan
F: phenylalanine
Y: tyrosine
L: leucine
V: valine
I: isoleucine
G: glycine
T: thréonine
S: serine
E: glutamic acid
D: Aspartic acid
N: asparagine
Q: glutamine
P: proline.
The asterisk signs “*” correspond to stop codons (i.e. TAA, TAG and TGA).
Starting above the first line of the DNA nucleotide sequence of FIG. 4, the three reading phases are respectively marked “1”, “2”, “3”, on the left handside of the drawing. The same relative presentation of the three theoretical reading phases is then used over all the successive lines of the LAV nucleotide sequence.
FIGS. 2 and 3 provide a diagrammatized representation of the lengths of the successive open reading frames corresponding to the successive reading phases (also referred to by numbers “1”, “2” and “3” appearing in the left handside part of FIG. 2. The relative positions of these open reading frames (ORF) with respect to the nucleotide structure of the LAV genome is referred to by the scale of numbers representative of the respective positions of the corresponding nucleotides in the DNA sequence. The vertical bars correspond to the positions of the corresponding stop codons.
1) The “gag gene” (or ORF-Gag)
The “gag gene” codes for core proteins. Particularly it appears that a genomic fragment (ORF-gag) thought to code for the core antigens including the p25, p18 and p13 proteins is located between nucleotide position 236 (starting with 5′ CTA GCG GAG 3′) and nucleotide position 1759 (ending by CTCG TCA CAA 3′). The structure of the peptides or proteins encoded by parts of said ORF is deemed to be that corresponding to phase 2.
The methionine amino acid “M” coded by the ATG at position 260–262 is the probable initiation methionine of the gag protein precursor. The end of ORF-gag and accordingly of gag protein appears to be located at position 1759.
The beginning of p25 protein, thought to start by a P-I-V-Q-N-I-Q-G-Q-M-V-H . . . amino acid sequence is thought to be coded for by the nucleotide sequence CCTATA . . . starting at position 656.
Hydrophilic peptides in the gag open reading frame are identified hereafter. They are defined starting from amino acid 1=Met (M) coded by the ATG starting from 260–2 in the LAV DNA sequence.
Those hydrophilic peptides are














12–32
amino acids
inclusive


37–46
′′
′′


49–79
′′
′′


 88–153
′′
′′


158–165
′′
′′


178–188
′′
′′


200–220
′′
′′


225–234
′′
′′


239–264
′′
′′


288–331
′′
′′


352–361
′′
′′


377–390
′′
′′


399–432
′′
′′


437–484
′′
′′


492–498
′′
′′









The invention also relates to any combination of these peptides.
2) The “pol gene” (or ORF-pol)
FIGS. 4–12 also show that the DNA fragments extending from nucleotide position 1555 (starting with 5′TTT TTT . . . 3′ to nucleotide position 5086 is thought to correspond to the pol gene. The polypeptidic structure of the corresponding polypeptides is deemed to be that corresponding to phase 1. It stops at position 4563 (end by 5′G GAT GAG GAT 3′).
These genes are thought to code for the virus polymerase or reverse transcriptase.
3) The Envelope Gene (or ORF-env)
The DNA sequence thought to code for envelope proteins is thought to extend from nucleotide position 5670 (starting with 5′AAA GAG GAG A . . . 3′) up to nucleotide position 8132 (ending by . . . A ACT AAA GAA 3′). Polypeptide structures of sequences of the envelope protein correspond to those read according to the “phase 3” reading phase.
The start of env transcription is thought to be at the level of the ATG codon at positions 5691–5693.
Additional features of the envelope protein coded by the env genes appear on FIGS. 13–18. These are to be considered as paired FIGS. 13 and 14; 15 and 16; 17 and 1, respectively.
It is to be mentioned that because of format difficulties,
FIG. 14 overlaps to some extent with FIG. 13.
FIG. 16 overlaps to some extent with FIG. 15,
FIG. 18 overlaps to some extent with FIG. 17.
Thus, for instance, FIGS. 13 and 14 must be considered together. Particularly the sequence shown on the first line on the top of FIG. 13 overlaps with the sequence shown on the first line on the top of FIG. 14. In other words, the starting of the reading of the successive sequences of the env gene as represented in FIGS. 13–18 involves first reading the first line at the top of FIG. 13 then proceeding further with the first line of FIG. 14. One then returns to the beginning of the second line of FIG. 13, then again further proceed with the reading of the second line of page 14. The same observations then apply to the reading of the paired FIGS. 15 and 16, and paired FIGS. 17 and 18, respectively.
The locations of neutralizing epitopes are further apparent in FIGS. 13–18. Reference is more particularly made to the boxed groups of three letters included in the amino acid sequences of the envelope proteins (reading phase 3) which can be designated generally by the formula N-X-S or N-X-T, wherein X is any other possible amino acid. Thus, the initial protein product of the env gene is a glycoprotein of molecular weight in excess of 91,000. These groups are deemed to generally carry glycosylated groups. These N-X-S and N-X-T groups with attached glycosylated groups form together hydrophilic regions of the protein and are deemed to be located at the periphery of and to be exposed outwardly with respect to the normal conformation of the proteins. Consequently, they are considered as being epitopes which can efficiently be brought into play in vaccine compositions.
The invention thus concerns with more particularity peptide sequences included in the env proteins and excisable therefrom (or having the same amino acid structure), having sizes not exceeding 200 amino acids.
Preferred peptides of this invention (referred to hereafter as a, b, c, d, e, f, are deemed to correspond to those encoded by the nucleotide sequences which extend, respectively, between the following positions:















a) from about 6095 to about 6200



b) from about 6260 to about 6310



c) from about 6390 to about 6440



d) from about 6485 to about 6620



e) from about 6860 to about 6930



f) from about 7535 to about 7630










Other hydrophilic peptides in the env open reading frame are identified hereafter. They are defined starting from amino acid 1=lysine (K) coded by the AAA at position 5670–2 in the LAV DNA sequence.
These hydrophilic peptides are














 8–23
amino acids
inclusive


63–78
′′
′′


82–90
′′
′′


 97–123
′′
′′


127–183
′′
′′


197–201
′′
′′


239–294
′′
′′


300–327
′′
′′


334–381
′′
′′


397–424
′′
′′


466–500
′′
′′


510–523
′′
′′


551–577
′′
′′


594–603
′′
′′


621–630
′′
′′


657–679
′′
′′


719–758
′′
′′


780–803
′′
′′









The invention also relates to any combination of these peptides.
4) The Other ORF
The invention further concerns DNA sequences which provide open reading frames defined as ORF-Q, ORF-R and as “1”, “2”, “3”, “4”, “5”, the relative position of which appears more particularly in FIGS. 2 and 3.
These ORFs have the following locations:


















ORF-Q
phase 1
start 4478
stop 5086



ORF-R
phase 2
start 8249
stop 8896



ORF-1
phase 1
start 5029
stop 5316



ORF-2
phase 2
start 5273
stop 5515



ORF-3
phase 1
start 5383
stop 5616



ORF-4
phase 2
start 5519
stop 5773



ORF-5
phase 1
start 7966
stop 8279










The LTR (long terminal repeats) can be defined as lying between position 8560 and position 160 (end extending over position 9097/1). As a matter of fact the end of the genome is at 9097 and, because of the LTR structure of the retrovirus, links up with the beginning of the sequence:




The invention concerns more particularly all the DNA fragments which have been more specifically referred to hereabove and which correspond to open reading frames. It will be understood that the man skilled in the art will be able to obtain them all, for instance by cleaving an entire DNA corresponding to the complete genome of a LAV species, such as by cleavage by a partial or complete digestion thereof with a suitable restriction enzyme and by the subsequent recovery of the relevant fragments. The different DNAs disclosed in the earlier mentioned British Application can be resorted to also as a source of suitable fragments. The techniques disclosed hereabove for the isolation of the fragments which were then included in the plasmids referred to hereabove and which were then used for the DNA sequencing can be used.
Of course methods can be used. Some of them have been exemplified in the earlier British Application. Reference is, for instance, made to the following methods.
a) DNA can be transfected into mammalian cells with appropriate selection markers by a variety of techniques, such as calcium phosphate precipitation, polyethylene glycol, protoplast-fusion, etc.
b) DNA fragments corresponding to genes can be cloned into expression vectors for E. coli, yeast or mammalian cells and the resultant proteins purified.
c) The proviral DNA can be “shot-gunned” (fragmented) into procaryotic expression vectors to generate fusion polypeptides. Recombinant producing antigenically competent fusion proteins can be identified by simply screening the recombinants with antibodies against LAV antigens.
The invention also relates more specifically to cloned probes which can be made starting from any DNA fragment according to this invention, thus to recombinant DNAs containing such fragments, particularly any plasmids amplifiable in procaryotic or eucaryotic cells and carrying said fragments.
Using the cloned DNA fragments as a molecular hybridization probe—either by marking with radionucleotides or with fluorescent reagents—LAV virion RNA may be detected directly in the blood, body fluids and blood products (e.g. of the antihemophilic factors, such as Factor VIII concentrates) and vaccines, i.e. hepatitis 8 vaccine. It has already been shown that whole virus can be detected in culture supernatants of LAV producing cells. A suitable method for achieving that detection comprises immobilizing virus onto a support, e.g. nitrocellulose filters, etc., disrupting the virion, and hybridizing with labelled (radiolabelled or “cold” fluorescent- or enzyme-labelled) probes. Such an approach has already been developed for Hepatitis 8 virus in peripheral blood (according to SCOTTO J. et al. Hepatology (1983), 3, 379–384).
Probes according to the invention can also be used for rapid screening of genomic DNA derived from the tissue of patients with LAV related symptoms to see if the proviral DNA or RNA is present in host tissue and other tissues.
A method which can be used for such screening comprises the following steps: extraction of DNA from tissue, restriction enzyme cleavage of said DNA, electrophoresis of the fragments and Southern blotting of genomic DNA from tissues, and sequent hybridization with labelled cloned LAV provival DNA. Hybridization in situ can also be used.
Lymphatic fluids and tissues and other non-lymphatic tissues of humans, primates and other mammalian species can also be screened to see if other evolutionary related retrovirus exist. The methods referred to hereabove can be used, although hybridization and washings would be done under non-stringent conditions.
The DNA according to the invention can also be used for achieving the expression of LAV viral antigens for diagnostic purposes.
The invention also relates to the polypeptides themselves which can be expressed by the different DNAs of the inventions, particularly by the ORFs or fragments thereof, in appropriate hosts, particularly procaryotic or eucaryotic hosts, after transformation thereof with a suitable vector previously modified by the corresponding DNAs.
These polypeptides can be used as diagnostic tools, particularly for the detection of antibodies in biological media, particularly in sera or tissues of persons afflicted with pre-AIDS or AIDS, or simply carrying antibodies in the absence of any apparent disorders. Conversely, the different peptides according to this invention can be used themselves for the production of antibodies, preferably monoclonal antibodies specific of the different peptides respectively. For the production of hybridomas secreting said monoclonal antibodies, conventional production and screening methods are used. These monoclonal antibodies, which themselves are part of the invention, then provide very useful tools for the identification and even determination of relative proportions of the different polypeptides or proteins in biological samples, particularly human samples containing LAV or related viruses.
Thus, all of the above peptides can be used in diagnostics as sources of immunogens or antigens free of viral particles, produced using non-permissive systems, and thus of little or no biohazard risk.
The invention further relates to the hosts (procaryotic or eucaryotic cells) which are transformed by the above-mentioned recombinants and which are capable of expressing said DNA fragments.
Finally, it also relates to vaccine compositions whose active principle is to be constituted by any of the expressed antigens, i.e. whole antigens, fusion polypeptides or oligopeptides, in association with a suitable pharmaceutically or physiologically acceptable carrier.
Preferably, the active principles to be considered in that field consist of the peptides containing less than 250 amino acid units, preferably less than 150 as deducible from the complete genomes of LAV, and even more preferably those peptides which contain one or more groups selected from N-X-S and N-X-T as defined above. Preferred peptides for use in the production of vaccinating principles are peptides (a) to (f) as defined above. By way of example having no limitative character, there may be mentioned that suitable dosages of the vaccine compositions are those which enable administration to the host, particularly human host, ranging from 10 to 500 micrograms per kg, for instance 50 to 100 micrograms per kg.
For the purpose of clarity, FIGS. 19 to 26 are added. Reference may be made thereto in case of difficulties of reading blurred parts of FIGS. 4 to 12.
Needless to say that FIGS. 19–26 are merely a reiteration of the whole DNA sequence of the LAV genome.
Finally, the invention also concerns vectors for the transformation of eucaryotic cells of human origin, particularly, lymphocytes, the polymerases of which are capable of recognizing the LTRs of LAV. Particularly said vectors are characterized by the presence of a LAV LTR therein, said LTR being then active as a promoter enabling the efficient transcription and translation in a suitable host of the above defined. DNA insert coding for a determined protein placed under its controls.
Needless to say that the invention extends to all variants of genomes and corresponding DNA fragments (ORFs) having substantially equivalent properties, all of said genomes belonging to retroviruses which can be considered as equivalents of LAV.

## Claims

1. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:









      5670       5680       5690       5700



         A AAGAGCAGAA GACAGTGGCA ATGAGAGTGA



 



      5710       5720       5730       5740



AGGAGAAATA TCAGCACTTG TGGAGATGGG GGTGGAAATG



 



      5750       5760       5770       5780



GGGCACCATG CTCCTTGGGA TATTGATGAT CTGTAGTGCT



 



      5790       5800       5810       5820



ACAGAAAAAT TGTGGGTCAC AGTCTATTAT GGGGTACCTG



 



      5830       5840       5850       5860



TGTGGAAGGA AGCAACCACC ACTCTATTTT GTGCATCAGA



 



      5870       5880       5890       5900



TGCTAAAGCA TATGATACAG AGGTACATAA TGTTTGGGCC



 



      5910       5920       5930       5940



ACACATGCCT GTGTACCCAC AGACCCCAAC CCACAAGAAG



 



      5950       5960       5970       5980



TAGTATTGGT AAATGTGACA GAAAATTTTA ACATGTGGAA



 



      5990       6000       6010       6020



AAATGACATG GTAGAACAGA TGCATGAGGA TATAATCAGT



 



      6030       6040       6050       6060



TTATGGGATC AAAGCCTAAA GCCATGTGTA AAATTAACCC



 



      6070       6080       6090       6100



CACTCTGTGT TAGTTTAAAG TGCACTGATT TGGGGAATGC



 



      6110       6120       6130       6140



TACTAATACC AATAGTAGTA ATACCAATAG TAGTAGCGGG



 



      6150       6160       6170       6180



GAAATGATGA TGGAGAAAGG AGAGATAAAA AACTGCTCTT



 



      6190       6200       6210       6220



TCAATATCAG CACAAGCATA AGAGGTAAGG TGCAGAAAGA



 



      6230       6240       6250       6260



ATATGCATTT TTTTATAAAC TTGATATAAT ACCAATAGAT



 



      6270       6230       6290       6300



AATGATACTA CCAGCTATAC GTTGACAAGT TGTAACACCT



 



      6310       6320       6330       6340



CAGTCATTAC ACAGGCCTGT CCAAAGGTAT CCTTTGAGCC



 



      6350       6360       6370       6380



AATTCCCATA CATTATTGTG CCCCGGCTGG TTTTGCGATT



 



      6390       6400       6410       6420



CTAAAATGTA ATAATAAGAC GTTCAATGGA ACAGGACCAT



 



      6430       6440       6450       6460



GTACAAATGT CAGCACAGTA CAATGTACAC ATGGAATTAG



 



      6470       6480       6490       6500



GCCAGTAGTA TCAACTCAAC TGCTGTTGAA TGGCAGTCTA



 



      6510       6520       6530       6540



GCAGAAGAAG AGGTAGTAAT TAGATCTGCC AATTTCACAG



 



      6550       6560       6570       6580



ACAATGCTAA AACCATAATA GTACAGCTGA ACCAATCTGT



 



      6590       6600       6610       6620



AGAAATTAAT TGTACAAGAC CCAACAACAA TACAAGAAAA



 



      6630       6640       6650       6660



AGTATCCGTA TCCAGAGGGG ACCAGGGAGA GCATTTGTTA



 



      6670       6680       6690       6700



CAATAGGAAA AATAGGAAAT ATGAGACAAG CACATTGTAA



 



      6710       6720       6730       6740



CATTAGTAGA GCAAAATGGA ATGCCACTTT AAAACAGATA



 



      6750       6760       6770       6780



GCTAGCAAAT TAAGAGAACA ATTTGGAAAT AATAAAACAA



 



      6790       6800       6810       6820



TAATCTTTAA GCAATCCTCA GGAGGGGACC CAGAAATTGT



 



      6830       6840       6850       6860



AACGCACAGT TTTAATTGTG GAGGGGAATT TTTCTACTGT



 



      6870       6880       6890       6900



AATTCAACAC AACTGTTTAA TAGTACTTGG TTTAATAGTA



 



      6910       6920       6930       6940



CTTGGAGTAC TGAAGGGTCA AATAACACTG AAGGAAGTGA



 



      6950       6960       6970       6980



CACAATCACA CTCCCATGCA GAATAAAACA ATTTATAAAC



 



      6990       7000       7010       7020



ATGTGGCAGG AAGTAGGAAA AGCAATGTAT GCCCCTCCCA



 



      7030       7040       7050       7060



TCAGCGGACA AATTAGATGT TCATCAAATA TTACAGGGCT



 



      7070       7080       7090       7100



GCTATTAACA AGAGATGGTG GTAATAACAA CAATGGGTCC



 



      7110       7120       7130       7140



GAGATCTTCA GACCTGGAGG AGGAGATATG AGGGACAATT



 



      7150       7160       7170       7180



GGAGAAGTGA ATTATATAAA TATAAAGTAG TAAAAATTGA



 



      7190       7200       7210       7220



ACCATTAGGA GTAGCACCCA CCAAGGCAAA GAGAAGAGTG



 



      7230       7240       7250       7260



GTGCAGAGAG AAAAAAGAGC AGTGGGAATA GGAGCTTTGT



 



      7270       7280       7290       7300



TCCTTGGGTT CTTGGGAGCA GCAGGAAGCA CTATGGGCGC



 



      7310       7320       7330       7340



ACGGTCAATG ACGCTGACGG TACAGGCCAG ACAATTATTG



 



      7350       7360       7370       7380



TCTGGTATAG TGCAGCAGCA GAACAATTTG CTGAGGGCTA



 



      7390       7400       7410       7420



TTGAGGCGCA ACAGCATCTG TTGCAACTCA CAGTCTGGGG



 



      7430       7440       7450       7460



CATCAAGCAG CTCCAGGCAA GAATCCTGGC TGTGGAAAGA



 



      7470       7480       7490       7500



TACCTAAAGG ATCAACAGCT CCTGGGGATT TGGGGTTGCT



 



      7510       7520       7530       7540



CTGGAAAACT CATTTGCACC ACTGCTGTGC CTTGGAATGC



 



      7550       7560       7570       7580



TAGTTGGAGT AATAAATCTC TGGAACAGAT TTGGAATAAC



 



      7590       7600       7610       7620



ATGACCTGGA TGGAGTGGGA CAGAGAAATT AACAATTACA



 



      7630       7640       7650       7660



CAAGCTTAAT ACATTCCTTA ATTGAAGAAT CGAAAACCA



 



      7670       7680       7690       7700



GCAAGAAAAG AATGAACAAG AATTATTGGA ATTAGATAAA



 



      7710       7720       7730       7740



TGGGCAAGTT TGTGGAATTG GTTTAACATA ACAAATTGGC



 



      7750       7760       7770       7780



TGTGGTATAT AAAAATATTC ATAATGATAG TAGGAGGCTT



 



      7790       7800       7810       7820



GGTAGGTTTA AGAATAGTTT TTGCTGTACT TTCTATAGTG



 



      7830       7840       7850       7860



AATAGAGTTA GGCAGGGATA TTCACCATTA TCGTTTCAGA



 



      7870       7880       7890       7900



CCCACCTCCC AACCCCGAGG GGACCCGACA GGCCCGAAGG



 



      7910       7920       7930       7940



AATAGAAGAA GAAGGTGGAG AGAGAGACAG AGACAGATCC



 



      7950       7960       7970       7980



ATTCGATTAG TGAACGGATC CTTAGCACTT ATCTGGGACG



 



      7990       8000       8010       8020



ATCTGCGGAG CCTTGTGCCT CTTCAGCTAC CACCGCTTGA



 



      8030       8040       8050       8060



GAGACTTACT CTTGATTGTA ACGAGGATTG TGGAACTTCT



 



      8070       8080       8090       8100



GGGACGCAGG GGGTGGGAAG CCCTCAAATA TTGGTGGAAT



 



      8110       8120       8130



CTCCTACAGT ATTGGAGTCA GGAACTAAAG AA.

2. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:








                                                             5700



                                                       ATGAGAGTGA


 


      5710       5720       5730       5740       5750       5760


AGGAGAAATA TCAGCACTTG TGGAGATGGG GGTGGAAATG GGGCACCATG CTCCTTGGGA


 


      5770       5780       5790       5800       5810       5820


TATTGATGAT CTGTAGTGCT ACAGAAAAAT TGTGGGTCAC AGTCTATTAT GGGGTACCTG


 


      5830       5840       5850       5860       5870       5880


TGTGGAAGGA AGCAACCACC ACTCTATTTT GTGCATCAGA TGCTAAAGCA TATGATACAG


 


      5890       5900       5910       5920       5930       5940


AGGTACATAA TGTTTGGGCC ACACATGCCT GTGTACCCAC AGACCCCAAC CCACAAGAAG


 


      5950       5960       5970       5980       5990       6000


TAGTATTGGT AAATGTGACA GAAAATTTTA ACATGTGGAA AAATGACATG GTAGAACAGA


 


      6010       6020       6030       6040       6050       6060


TGCATGAGGA TATAATCAGT TTATGGGATC AAAGCCTAAA GCCATGTGTA AAATTAACCC


 


      6070       6080       6090       6100       6110       6120


CACTCTGTGT TAGTTTAAAG TGCACTGATT TGGGGAATGC TACTAATACC AATAGTAGTA


 


      6130       6140       6150       6160       6170       6180


ATACCAATAG TAGTAGCGGG GAAATGATGA TGGAGAAAGG AGAGATAAAA AACTGCTCTT


 


      6190       6200       6210       6220       6230       6240


TCAATATCAG CACAAGCATA AGAGGTAAGG TGCAGAAAGA ATATGCATTT TTTTATAAAC


 


      6250       6260       6270       6230       6290       6300


TTGATATAAT ACCAATAGAT AATGATACTA CCAGCTATAC GTTGACAAGT TGTAACACCT


 


      6310       6320       6330       6340       6350       6360


CAGTCATTAC ACAGGCCTGT CCAAAGGTAT CCTTTGAGCC AATTCCCATA CATTATTGTG


 


      6370       6380       6390       6400       6410       6420


CCCCGGCTGG TTTTGCGATT CTAAAATGTA ATAATAAGAC GTTCAATGGA ACAGGACCAT


 


      6430       6440       6450       6460       6470       6480


GTACAAATGT CAGCACAGTA CAATGTACAC ATGGAATTAG GCCAGTAGTA TCAACTCAAC


 


      6490       6500       6510       6520       6530       6540


TGCTGTTGAA TGGCAGTCTA GCAGAAGAAG AGGTAGTAAT TAGATCTGCC AATTTCACAG


 


      6550       6560       6570       6580       6590       6600


ACAATGCTAA AACCATAATA GTACAGCTGA ACCAATCTGT AGAAATTAAT TGTACAAGAC


 


      6610       6620       6630       6640       6650       6660


CCAACAACAA TACAAGAAAA AGTATCCGTA TCCAGAGGGG ACCAGGGAGA GCATTTGTTA


 


      6670       6680       6690       6700       6710       6720


CAATAGGAAA AATAGGAAAT ATGAGACAAG CACATTGTAA CATTAGTAGA GCAAAATGGA


 


      6730       6740       6750       6760       6770       6780


ATGCCACTTT AAAACAGATA GCTAGCAAAT TAAGAGAACA ATTTGGAAAT AATAAAACAA


 


      6790       6800       6810       6820       6830       6840


TAATCTTTAA GCAATCCTCA GGAGGGGACC CAGAAATTGT AACGCACAGT TTTAATTGTG


 


      6850       6860       6870       6880       6890       6900


GAGGGGAATT TTTCTACTGT AATTCAACAC AACTGTTTAA TAGTACTTGG TTTAATAGTA


 


      6910       6920       6930       6940       6950       6960


CTTGGAGTAC TGAAGGGTCA AATAACACTG AAGGAAGTGA CACAATCACA CTCCCATGCA


 


      6970       6980       6990       7000       7010       7020


GAATAAAACA ATTTATAAAC ATGTGGCAGG AAGTAGGAAA AGCAATGTAT GCCCCTCCCA


 


      7030       7040       7050       7060       7070       7080


TCAGCGGACA AATTAGATGT TCATCAAATA TTACAGGGCT GCTATTAACA AGAGATGGTG


 


      7090       7100       7110       7120       7130       7140


GTAATAACAA CAATGGGTCC GAGATCTTCA GACCTGGAGG AGGAGATATG AGGGACAATT


 


      7150       7160       7170       7180       7190       7200


GGAGAAGTGA ATTATATAAA TATAAAGTAG TAAAAATTGA ACCATTAGGA GTAGCACCCA


 


      7210       7220       7230       7240       7250       7260


CCAAGGCAAA GAGAAGAGTG GTGCAGAGAG AAAAAAGAGC AGTGGGAATA GGAGCTTTGT


 


      7270       7280       7290       7300       7310       7320


TCCTTGGGTT CTTGGGAGCA GCAGGAAGCA CTATGGGCGC ACGGTCAATG ACGCTGACGG


 


      7330       7340       7350       7360       7370       7380


TACAGGCCAG ACAATTATTG TCTGGTATAG TGCAGCAGCA GAACAATTTG CTGAGGGCTA


 


      7390       7400       7410       7420       7430       7440


TTGAGGCGCA ACAGCATCTG TTGCAACTCA CAGTCTGGGG CATCAAGCAG CTCCAGGCAA


 


      7450       7460       7470       7480       7490       7500


GAATCCTGGC TGTGGAAAGA TACCTAAAGG ATCAACAGCT CCTGGGGATT TGGGGTTGCT


 


      7510       7520       7530       7540       7550       7560


CTGGAAAACT CATTTGCACC ACTGCTGTGC CTTGGAATGC TAGTTGGAGT AATAAATCTC


 


      7570       7580       7590       7600       7610       7620


TGGAACAGAT TTGGAATAAC ATGACCTGGA TGGAGTGGGA CAGAGAAATT AACAATTACA


 


      7630       7640       7650       7660       7670       7680


CAAGCTTAAT ACATTCCTTA ATTGAAGAAT CGAAAACCA  GCAAGAAAAG AATGAACAAG


 


      7690       7700       7710       7720       7730       7740


AATTATTGGA ATTAGATAAA TGGGCAAGTT TGTGGAATTG GTTTAACATA ACAAATTGGC


 


      7750       7760       7770       7780       7790       7800


TGTGGTATAT AAAAATATTC ATAATGATAG TAGGAGGCTT GGTAGGTTTA AGAATAGTTT


 


      7810       7820       7830       7840       7850       7860


TTGCTGTACT TTCTATAGTG AATAGAGTTA GGCAGGGATA TTCACCATTA TCGTTTCAGA


 


      7870       7880       7890       7900       7910       7920


CCCACCTCCC AACCCCGAGG GGACCCGACA GGCCCGAAGG AATAGAAGAA GAAGGTGGAG


 


      7930       7940       7950       7960       7970       7980


AGAGAGACAG AGACAGATCC ATTCGATTAG TGAACGGATC CTTAGCACTT ATCTGGGACG


 


      7990       8000       8010       8020       8030       8040


ATCTGCGGAG CCTTGTGCCT CTTCAGCTAC CACCGCTTGA GAGACTTACT CTTGATTGTA


 


      8050       8060       8070       8080       8090       8100


ACGAGGATTG TGGAACTTCT GGGACGCAGG GGGTGGGAAG CCCTCAAATA TTGGTGGAAT


 


      8110       8120       8130


CTCCTACAGT ATTGGAGTCA GGAACTAAAG AA.

3. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:








                                      6100        6110        6120



                                    GAATGC  TACTAATACC  AATAGTAGTA


 


      6130       6140       6150       6160       6170       6180


ATACCAATAG TAGTAGCGGG GAAATGATGA TGGAGAAAGG AGAGATAAAA AACTGCTCTT


 


      6190       6200


TCAATATCAG CACAAGCATA.

4. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:









      6260       6270       6280       6290



         T AATGATACTA CCAGCTATAC GTTGACAAGT



 



      6300       6310



TGTAACACCT CAGTCATTAC.

5. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:









      6390       6400       6410       6420



         A ATAATAAGAC GTTCAATGGA ACAGGACCAT



 



      6430       6440



GTACAAATGT CAGCACAGTA.

6. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:








      6490       6500       6510       6520       6530       6540



    GTTGAA TGGCAGTCTA GCAGAAGAAG AGGTAGTAAT TAGATCTGCC AATTTCACAG


 


      6550       6560       6570       6580       6590       6600


ACAATGCTAA AACCATAATA GTACAGCTGA ACCAATCTGT AGAAATTAAT TGTACAAGAC


 


      6610       6620


CCAACAACAA TACAAGAAAA.

7. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:









      6860       6870       6880       6890



         T AATTCAACAC AACTGTTTAA TAGTACTTGG



 



      6900       6910       6920       6930



TTTAATAGTA CTTGGAGTAC TGAAGGGTCA AATAACACTG.

8. A cloned DNA of Human Immunodeficiency Virus Type 1 (HIV-1), wherein the DNA comprises the sequence CTCAATAAAGCTTGCCTTG, and the DNA comprises the sequence:








                                        7540       7550       7560



                                      GAATGC TAGTTGGAGT AATAAATCTC


 


       7570       7580       7590       7600       7610       7620


 TGGAACAGAT TTGGAATAAC ATGACCTGGA TGGAGTGGGA CAGAGAAATT AACAATTACA


 


      7630


CAAGCTTAAT.

9. A method of using the cloned DNA of any of claims 1–8 to detect HIV-1 RNA comprising:
(a) providing a biological fluid comprising HIV-1 infected cells;
(b) preparing a cell-free supernatant from the biological fluid;
(c) isolating HIV-1 virions from the cell-free supernatant;
(d) disrupting the virions to release HIV-1 RNA;
(e) contacting the HIV-1 RNA with the HIV-1 DNA of any of claims 1–8; and
(f) detecting hybridization between the HIV-1 RNA and the HIV-1 DNA.

10. A method of making HIV-1 RNA comprising:
(a) providing a biological fluid comprising HIV-1 infected cells;
(b) preparing a cell-free supernatant from the biological fluid;
(c) isolating HIV-1 virions from the cell-free supernatant; and
(d) disrupting the virions to release HIV-1 RNA, thereby making HIV-1 RNA.