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1、HIV-2 isolate ALI from Guinea-Bissau, plete genomeLOCUS AF082339 10353 bp DNA linear VRL 13-DEC-1998DEFINITION HIV-2 isolate ALI from Guinea-Bissau, plete genome.ACCESSION AF082339VERSION AF082339.1 GI:4007991KEYWORDS .SOURCE Human immunodeficiency virus 2 (HIV-2) ORGANISM Human immunodeficiency vir
2、us 2 Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus group.REFERENCE 1 (bases 1 to 10353) AUTHORS Azevedo-Pereira,J.M., Goncalves,J., Freitas-Vieira,A., Vital,J., Santos-Costa,Q. and Moniz-Pereira,J. TITLE plete nucleotide sequence of HIV-2ALI, a
3、low infectious isolate with restricted tropism to primary CD4+ cells JOURNAL UnpublishedREFERENCE 2 (bases 1 to 10353) AUTHORS Azevedo-Pereira,J.M., Goncalves,J., Freitas-Vieira,A., Vital,J., Santos-Costa,Q. and Moniz-Pereira,J. TITLE Direct Submission JOURNAL Submitted (04-AUG-1998) Microbiology, F
4、ac Pharmacy of Lisbon, Avenue Forcas Armadas, Lisbon 1600, PortugalFEATURES Location/Qualifiers source 1.10353 /organism=Human immunodeficiency virus 2 /proviral /mol_type=genomic DNA /strain=HIV-2ALI /isolate=ALI /db_*ref=ta*on:11709 /country=Guinea-Bissau /note=primary isolate recovered from a sym
5、ptomatic patient; differentiating biological characteristics pared to other HIV-2: low infectivity in vitro, persistent incapability to induce syncytia formation, e*tremely narrow cellular host range; virus was only passaged twice in human PBMC before chromosomal DNA from infected cells was harveste
6、d; direct PCR was performed to obtain the total proviral DNA in four overlapping fragments that were cloned into plasmid vector pCR3; both strands of proviral DNA were pletely sequenced; the HIV-2 ALI genome reveals a similar localization of the open reading frames for structural, regulatory and acc
7、essory genes, pared to other HIV-2 viruses repeat_region 1.850 /note=5 long terminal repeat /rpt_type=long_terminal_repeat gene 1096.2661 /gene=gag CDS 1096.2661 /gene=gag /note=encodes structural proteins of HIV-2 ALI nucleocapside /codon_start=1 /product=gag protein /protein_id=AAC95340.1 /db_*ref
8、=GI:4007992 /translation=MGARNSVLRGRKADELERIRLRPGGKKKYQLKHIVWAANELDRF GLAESLLESKEGCQRILKVLEPLVPTGSENLKSLFNTVCVVWCVHAEEKVKDTEGAKQ IIQRHLAAEIETAEKMPSTSRPTAPPSEQGGNFPVQQVAGNYTHVPLSPRTLDAWVKL VEEKKFGAEVVPGFQALSEGCTPYDINQMLNCVGDHQAAMQIIREIINEEAADWDVAH PIPGPLPAGQLREPRGSDIAGTTSTVEEQIQWMFRPRNPVPVGNIYRRWIQIG
9、LQKCV RMYNPTNILDIKQGPKEPFQSYVDRFYKSLRAEQTDPAVKNWMTQTLLVQNANPDCKL VLKGLGMNPTLEEMLTACQGVGGPGQKARLMAEALKEAMTPAPIPFAAAQQRRTIKCW NCGKEGHSARQCRAPRKQGCWKCGKPGHLMANCPERQAGFLGLGPWGKKPRNFPVTRV PQGLTPTAPPAEPAADLLEQYMQQGRKQREQRERPYKEVTEDLLHLEQGETPHKEVTE DLLHLNSLFGKDQ gene 2319.5486 /gene=pol CDS 2319.5486 /gene
10、=pol /note=encodes protease, reverse transcriptase and integrase /codon_start=1 /product=pol polyprotein /protein_id=AAC95341.1 /db_*ref=GI:4007993 /translation=KTGLLEMWQARTSYGKLPRKTGWFFRAWPMGKEASQLPRNPSSA GINTNSTPSRASSGPAGAVYAAGEKAKRAEREAIQRGDGGLTAPRAGRDTTQRGDRGL AAPQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIV
11、AGIELGSNYTPKIVGGIGGFINT KEYEDVEIKVLNKRVKATIMTGDTPINIFGRNILTALGMSLNLPVAKIEPIEVRLKPG KDGPKLRQWPLTKEKIEALKEICEKTEREGQLEEAPPTNPYNTPTFAIKKKDKNKWRM LIDFRELNKVTQDFTEIQLGIPHPAGLAKKRRITVLDVGDAYFSIPLHESFRQYTAFT LPSVNNAEPGKRYIYKVLPQGWKGSPAIFQHTMRQILEPFRKANQDVILIQYMDDILI ASDRTDLEHDKVVLQLKELLNGLGFSTPDEKFQKDPPYKW
12、MGYGLWPTKWKLQKIQLP QKEVWTVNDIQKHVGVLNWAAQIYPGIKTKHLCRLIRGKMTLTEGVQWTELAEAELEE NRIILSQEQEGHYYQEEKELEATVQKDQDNQWTYKIHQGEKILKVEKYAKMKNTHTNG VRLLAQVVQKIGKEALVIWGRIPRFHLPVERETWEQWWDDYWQVTWIPDWDFVSTPPL VRLAFNLVKDPILGAETFYTDGPRQSKEGKAGYITDRGRDKVKVLEQTTNQQAELE AFALAVTDSGPKANIIVDSQYVMGIVAGQPTESENRIVNQIIEEMIK
13、KEAIYVAWVPA HKGIGGNQEVDHLVSQGIRQVLFLEKIEPAQEEHEKYHSNVKELSHKFGLPNLVARQI VNTCAQCQQKGEAIHGQVNAELGTWQMDCTHLEGKVIIIAVHVASGFIEAEVIPQESG RQTALFLLKLASRWPITHLHTDSGVNFTSQEVKMVAWWVGIEQSFGVPYNPQSQGVVE AMNHHLKNQISRIREQANTVETIVLMAVHCMNFKRRGGIGDMTPAERLINMISTEQEI QFLQTKNLKFKNFPVYYREGRDQLWKGPGELLWKGDGAVIVKVGTDIKVVPR
14、RKAKII RDYGGRQELDSGPHLEGAREDGEVA gene 5416.6063 /gene=vif CDS 5416.6063 /gene=vif /function=accessory protein /codon_start=1 /product=vif protein /protein_id=AAC95342.1 /db_*ref=GI:4007994 /translation=MEEGKSWIVVPTWRVPGRMEKWHSLVKYLKYRTKDLEKVCYVPH HKVGWAWWTCSRVIFPLQGRSHLEIQAYWNLTPEKGWLSSYAVRITWYTEKFW
15、TDVTP DCADSLIHGTYFSCFTAGEVRRAIRGEKLLSCYPQAHKSQVPSLQFLALVVVQQNG KPQRNSTTRKQWRRDYRRGLRVARQDSRGLKQRGGESPAPGAHFPGVAKVLEILA gene 5891.6229 /gene=vp* CDS 5891.6229 /gene=vp* /function=accessory protein /codon_start=1 /product=vp* protein /protein_id=AAC95343.1 /db_*ref=GI:4007995 /translation=MANPRETVPPGN
16、SGEETIGEAFEWLDRTVEALNREAVNHLPREL IFQVWQRSWRYWHDEQGMSQSYTKYRYLCLMQKAMYTHFMKGCTCLGGGHGPGGWRSG PPPPPPPGLV gene 6229.6546 /gene=vpr CDS 6229.6546 /gene=vpr /note=accessory protein /codon_start=1 /product=vpr protein /protein_id=AAC95344.1 /db_*ref=GI:4007996 /translation=MTEAPTEFPPAGMGPHQGARDEWVIEVLREIK
17、EEALRHFDPRML IALGGYIYTRHGDTLERARELINALQRALFMHFRAGCGRSRVGQTRGRNPLSAIPTPR NMQ gene 6392.8959 /gene=tat CDS join(6392.6687,8845.8959) /gene=tat /function=regulatory protein /codon_start=1 /product=tat protein /protein_id=AAC95345.1 /db_*ref=GI:4007997 /translation=METPLKEPGSSLMPYNEPSSCTSEQDVAVQELAKQGEE
18、ILSQLY RPLETNTCYCKECCYHCQLCFLNKGLGIWYDRKGRRRRSPKKIKAHSSSASDKSIS TRTRNSQPEEKQKKTLETTLGTDCGPGRSHIYIS gene 6618.9098 /gene=rev CDS join(6618.6687,8845.9098) /gene=rev /function=regulatory protein /codon_start=1 /product=rev protein /protein_id=AAC95346.1 /db_*ref=GI:4007998 /translation=MTERAGEEDLQRKLR
19、LIRLLHQTNPYPQGPGTANQRRNRRRRWR QRWGQIVALADRIFTFPDPPASSPLDRAVQHLQGLTIQDLPDPPTDLPESSESADNNQ GLAET gene 6694.9282 /gene=env CDS 6694.9282 /gene=env /codon_start=1 /product=envelope glycoprotein /protein_id=AAC95347.1 /db_*ref=GI:4007999 /translation=MMSSRNQLLVTILLASACLVYCKQYVTVFYGVPAWKNASIPLFC ATKNRDTWG
20、TIQCLPDNDDYQEIALNVTEAFDAWDNTVTEQAVEDVWRLFETSIKPCV KLTPLCIAMKCSNISTESTTTSPSPGSTLKPLINESDPCIKADNCPRGLGDEEMVNCR FNMTGLQRDKPKQYNETWYSKDVVCEPFNTTTNQTRCYMNHTSVITESCDKHYWDA IRFRYCAPPGYALLRCDDINYSGFAPNCSKVVAATCTRMMETQTSTWFGFNGTRAENR TYIYWHGRDNRTIISLNKHYNLTMHCKRPGNKTVVPITLMSGLIFHSQPINKRPRQAW CWFKGEWRKAMQEVKE
21、TLVKHPRYKGTNDTNQINFTKPGRGSDAEVVYMWTNCRGEFL HMTWFLNWVENKTGQEQHNYAPCHIKQIINIWHKAGKNVYLPPREGELTSTVTS LIANIDTDGNQTNITFSAEVAELYRLELGDYKLVEITPIGFAPTSERRYSSTPRRNKR GVFVLGFLGFLATAGSAMGTAALTLSAQSRTLLAGIVQQQQQLLDVVKRQQEMLRLTV WGTKNLQARVTAIEKYLKDQARLNSWGCAFRQVCHTTVPWVNNSLKPDWDNMTWQEWE QQVRYLEANISEQLERAQIQQEKNT
22、YELQKLNSWDVFTNWLDLTAWVKYIQYGVYIIV GIVALRIVIYVVQMLSRLRKGYRPVFSSPPGYIQQIHIHKDQEQPTRGETEEDVGDNV GDRLWPWPIAYLHFLIHLLARLLIGLYSICRDLLSRISPILQPIFRSLQRALTTIRDW LRLKAAYLQYGCEWIQEAFRAFARIARETLTNTWRDLWGAVQWVGRRILAVPRRIRQG AEIALL gene 9116.9904 /gene=nef CDS 9116.9904 /gene=nef /function=accessory protein /codo
23、n_start=1 /product=nef protein /protein_id=AAC95348.1 /db_*ref=GI:4008000 /translation=MGASGSKKRSGPLQGLRERLLQTPGETCGGQCSGSGGGYSQSQG GSGRGQKLPSCEGQRYQQGDFMNTPWRTPATEREKELYKQQNMDDVDLDDDDSLVGVS VTPRVQLRTMTYKLAVDMSHLIKERGGLEGMFYSERRHRILDIYLEKEEGIIPDWQNY THGPGIRYPMFFGWLWKLVPVDVPQEGEDTETHCLLHPVQTSRHDDTHGE
24、TLVWRFDP KLAHDYKAFILHPEEFGYKSGLPEDEWKARLKARGIPFSKNRNS repeat_region 9504.10353 /note=3 long terminal repeat /rpt_type=long_terminal_repeatORIGIN 1 tggaagggat gttttacagt gagagaagac atagaatctt agacatatac ttagaaaagg 61 aagaagggat aattccagat tggcagaact atactcatgg gccaggaata aggtacccga 121 tgttctttgg gtg
25、gctgtgg aagctagtac cagtagatgt cccacaagaa ggggaggaca 181 ctgagactca ctgcctgcta cacccagtac aaacaagcag gcatgatgac acgcatgggg 241 agacattagt ttggagattt gaccctaagc tggctcatga ttacaaagcc tttattctac 301 acccagagga atttgggtac aagtcaggcc tgccagaaga tgagtggaag gcaagactga 361 aagcaagagg gataccattt agtaagaaca g
26、gaacagctg atttggtcag ggcaggaagt 421 aactactgaa aacagctgag actgcaggga ctttccagaa ggggctgtaa ccaggggaag 481 gacatgggag gagctggtgg ggaacgccct catactcctg tataaatgta cccgctgctt 541 gcattgtatt cagtcgctct gcggagaggc tggcagattg agccctggga ggttctctcc 601 agcactagca ggtagagcct gggtgttccc tgctagactc tcaccagtgc
27、 ttggccggca 661 ctgggcagac ggctccacgc ttgcttgctt aaagacctct taataaagct gccaattaga 721 agcaggttaa aggtgtgttc ccatctctcc tagtcgccgc ctggtcattc ggtgttcacc 781 tgagtaacaa gaccctggtc tgttaggacc ctttctgctt tgggaaacgg aggcaggaaa 841 atccctagca ggttggcgcc cgaacaggga cttgaagaag actgagaagt ctaggaacac 901 ggct
28、gagtga aggcagtaag ggcggcagga acaaaccacg acggagtgct cctagaaagg 961 cgcaggccaa ggtaccaaag gccggcgtgt ggagcgggag tgaagaggcc tccgggtgaa 1021 ggtaagtacc tacaccaaaa ttgtagccga aagggcttgt tatcctacct ttagacaggt 1081 agaagattgt gggagatggg cgcgagaaac tccgtcttga gagggagaaa agcagacgaa 1141 ttagaaagaa ttaggttacg
29、 gcccggcgga aagaaaaaat atcagctaaa acatattgtg 1201 tgggcagcga atgaattgga cagattcgga ttggcagaaa gcctgttgga gtcaaaagaa 1261 ggttgccaaa gaattcttaa agttttagaa ccattagtgc caacaggatc agaaaattta 1321 aaaagccttt ttaatactgt ctgcgtagtt tggtgcgtgc acgcagaaga gaaagtgaaa 1381 gatactgaag gagcaaaaca aataatacag agac
30、atctag cggcagaaat agaaacagca 1441 gagaaaatgc caagcacaag tagaccaaca gcaccaccta gtgaacaggg gggaaacttc 1501 cccgtacaac aagtagccgg caactacacc catgtgccgc tgagcccccg aaccttagat 1561 gcttgggtaa aattagtaga agaaaagaag ttcggggcag aagtagtgcc aggatttcag 1621 gcactctcag aaggctgcac gccctatgat attaatcaaa tgcttaatt
31、g tgtgggcgac 1681 catcaagcag ccatgcaaat aatcagggag attatcaatg aagaagcagc agactgggat 1741 gttgcacatc ccataccagg ccccttacca gcagggcagc ttagagaacc aagagggtct 1801 gacatagcag gaacaacaag cacagtagaa gaacagatcc agtggatgtt caggccacgg 1861 aatcctgtgc cagtagggaa catctataga agatggatcc agatagggct acagaagtgt 192
32、1 gtcaggatgt acaacccaac caacatccta gacataaaac aaggaccaaa ggagccattc 1981 caaagctatg tagatagatt ctacaaaagc ttaagggcag aacaaacaga tccagcagta 2041 aagaattgga tgactcaaac actgctggta cagaatgcca acccagactg caaattagtg 2101 ctgaaaggat tagggatgaa tcctacctta gaagagatgc taaccgcctg tcagggagta 2161 gggggaccag gcc
33、agaaagc cagattaatg gcagaagcct taaaggaggc catgacacca 2221 gctcctatcc catttgcggc agcccaacaa agaaggacaa ttaagtgctg gaattgtgga 2281 aaggaagggc actcggcaag acaatgccga gcacccagaa aacagggctg ctggaaatgt 2341 ggcaagccag gacatcttat ggcaaactgc ccagaaagac aggctggttt tttagggctt 2401 ggcccatggg gaaagaagcc tcgcaact
34、tc cccgtaaccc gagttccgca gggattaaca 2461 ccaacagcac ccccagcaga gccagcagcg gacctgctgg agcagtatat gcagcagggg 2521 agaaagcaaa gagagcagag agagaggcca tacaaagagg tgacggagga cttactgcac 2581 ctcgagcagg gagagacacc acacaaagag gtgacagagg acttgctgca cctcaattct 2641 ctctttggaa aagaccagta gtcacagcct acattgaggg cc
35、agccagtg gaagttttac 2701 tagacacagg ggctgacgac tcaatagtag caggaataga gttagggagc aactataccc 2761 caaaaatagt agggggaata gggggattca taaataccaa agaatatgaa gatgtagaaa 2821 taaaagtact aaataaaaga gtaaaagcca ccataatgac aggtgacacc ccaatcaata 2881 tttttggcag aaacattttg acagccttag gcatgtcatt aaacctacca gttgccaaga 2941 tagagccaat agaggtaaga ttaaagccag gaaaagacgg gccaaaatta agacaa
