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LOCUS	    KF527090		    4682 bp    RNA     linear	VRL 02-SEP-2013
DEFINITION  HIV-1 isolate 4419_311 from Malawi pol protein (pol) gene, partial
	    cds; and vif protein (vif), vpr protein (vpr), tat protein (tat),
	    rev protein (rev), vpu protein (vpu), envelope glycoprotein (env),
	    and nef protein (nef) genes, complete cds
ACCESSION   KF527090
VERSION     KF527090.1 GI:534805114
KEYWORDS    .
SOURCE	    Human immunodeficiency virus 1 (HIV-1)
  ORGANISM  Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
	    Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
	    group
REFERENCE   1 (bases 1 to 4682)
            Show all sequences for reference 1
  AUTHORS   Permar,S.R., Salazar,M.G., Gao,F., Cai,F., Learn,G.H., Kalilani,L.,
	    Hahn,B.H., Shaw,G.M. and Salazar-Gonzalez,J.F.
  TITLE     Clonal amplification and maternal-infant transmission of
	    nevirapine-resistant HIV-1 variants in breast milk following
	    single-dose nevirapine prophylaxis
  JOURNAL   Retrovirology 10, 88 (2013)
  PUBMED    23941304
REFERENCE   2 (bases 1 to 4682)
            Show all sequences for reference 2
  AUTHORS   Permar,S., Salazar,M., Gao,F., Cai,F., Learn,G., Kalilani,L.,
	    Hahn,B., Shaw,G. and Salazar-Gonzalez,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-AUG-2013) Medicine, University of Alabama at
	    Birmingham, 720 20th Street South, Birmingham, AL 35294, USA
COMMENT     Annotation information was provided by the author. Some of the
	    information does not have GenBank feature identifiers and is being
	    provided in the comment section. Information in this section is
	    searchable in HIV Database at Los Alamos (hiv.lanl.gov).;
	    ##HIVDataBaseData-START## Patient code 714904419 Sample city
	    Blantyre Patient Cohort CHAVI 009 Patient sex M Risk factor MB
	    Viral load 1210000 Patient health status acute infection Sample
	    timepoint 12 weeks of age Sample tissue plasma Culture method
	    uncultured Amplification Strategy single genome amplification
	    Patient comment Postnatally infected infant via breastfeeding
	    ##HIVDataBaseData-END##
FEATURES             Location/Qualifiers
     source	     1..4682
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="4419_311"
		     /host="Homo sapiens"
		     /db_xref="taxon:11676"
		     /country="Malawi"
		     /collection_date="15-Aug-2008"
		     /note="plasma sample taken at 12 weeks of age when first
		     detected HIV DNA PCR positive; subtype: C"
     gene	     <1..173
		     /gene="pol"
     CDS	     <1..173
		     /gene="pol"
		     /codon_start="3"
		     /transl_table="1"
		     /product="pol protein"
		     /protein_id="AGU35811.1"
		     /db_xref="GI:534805115"
		     /translation="PIWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKVKIIKDYGKQMA
		     GADCVAGRQDED"
     gene	     118..696
		     /gene="vif"
     CDS	     118..696
		     /gene="vif"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vif protein"
		     /protein_id="AGU35812.1"
		     /db_xref="GI:534805116"
		     /translation="MENRWQVLIVWQVDRMRIRTWNSLVKHHMYVSRRAHGWFYRHHY
		     ESRHPKISSEVHIPLGEARLVIKTYWGLQTGEREWHLGHGVSIEWRLRRYSTQVDPGL
		     ADQLIHMHYFDCFADSAIRKAILGHIVIPRCDYQAGHNKVGSLQYLALTALIKPKKRK
		     PPLPSVRKLVEDRWNNPQKTRGRRGNHTMNGH"
     gene	     636..926
		     /gene="vpr"
     CDS	     636..926
		     /gene="vpr"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpr protein"
		     /protein_id="AGU35813.1"
		     /db_xref="GI:534805117"
		     /translation="MEQPPEDQGPQREPYNEWTLEILEELKQEAVRHFPIPWLHNLGQ
		     YIYETYGDTWAGVEAIIKILQQLLFIHFRIGCQHSRIGILRQRRARNGANRS"
     gene	     907..3536
		     /gene="tat"
     CDS	     join(907..1121,3446..3536)
		     /gene="tat"
		     /codon_start="1"
		     /transl_table="1"
		     /product="tat protein"
		     /protein_id="AGU35814.1"
		     /db_xref="GI:534805118"
		     /translation="MEPIDPKLEPWNHPGSKPKTACNNCYCKCCSYHCLVCFQTKGLG
		     ISYGRKKRRQRRRAPPSSEDHQNPISKQPLPQARGDPTGSEESKKKVESKTETDPFD"
     gene	     1046..3693
		     /gene="rev"
     CDS	     join(1046..1121,3446..3693)
		     /gene="rev"
		     /codon_start="1"
		     /transl_table="1"
		     /product="rev protein"
		     /protein_id="AGU35815.1"
		     /db_xref="GI:534805119"
		     /translation="MAGRSGDSDEGLLQAVRIIKILYQSNPYPKPEGTRQARKNRRRR
		     WRARQRQIHSISERILSTCLGRPAEPVPLPLPPIERLSIGDSENGGNSGTQQSQGTTE
		     GVGSP"
     gene	     1135..1395
		     /gene="vpu"
     CDS	     1135..1395
		     /gene="vpu"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpu protein"
		     /protein_id="AGU35816.1"
		     /db_xref="GI:534805120"
		     /translation="MSSLIEKVDYRVGIAALIIALLIAIVVWIIVYIEYRKLLRQRKI
		     DWLVERIRERAEDSGNESEGDIEELATMGDMGHLRLLDGVDL"
     gene	     1313..3883
		     /gene="env"
     CDS	     1313..3883
		     /gene="env"
		     /codon_start="1"
		     /transl_table="1"
		     /product="envelope glycoprotein"
		     /protein_id="AGU35817.1"
		     /db_xref="GI:534805121"
		     /translation="MRVRGILRSWQPWGIWGILGFWMVLTCSVLGNLWVTVYYGVPVW
		     KEAKTTLFCASDAKAYEREMHNVWATHACVPTDPNPQELVLENVTENFNMWKNDMVDQ
		     MHEDIISLWDQSLKPCVKLTPLCVTLDCKNSTENITDSRNITDNGERKNCSFNITTEI
		     KDKKQNVYALFYKLDIVPLHEDNSSYYRLINCNTSAITQACPKVSFDPIPIHYCAPAG
		     YAILKCNNKTFNGTGPCHNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSKDLTDN
		     AKIIIVHLNKSVEINCTRPGNNTRKSIRIGPGQTFYAPNGIIGNIRKAHCNIKGKQWN
		     ETLIKVGEKLAELFPNKIIKFNSSSGGDLEITTHSFNCGGEFFYCDTSGLFNGTYNPN
		     DTTSNSSSLNNITLTLPCKIKQVINMWQGVGKAIYAPPIAGNITCRSNITGLLLLRDG
		     GTTNDTEEIFRPGGGDMRDNWRSELYKYKVVEIKPLGVAPTKAKRRVVEREKRAVGIG
		     AVLLGFLGAAGSTMGAASITLTVQARQLLSGIVQQQSNLLRAIEAQQHMLQLTVWGIK
		     QLQARVLAIERYLKDQQLLGIWGCSGKLICTTSVPWNDSWSHNKSLQDIWDNMTWMQW
		     DKEINNYTSTIYRLLEESQNQQEKNEQDLLALDSWQNLWNWFSISKWLWYIKIFIMIV
		     GGLIGLRIIFAVLSIVNRVRQGYSPLSFQTLTPSPRGPDRLGRIEEEGGEQDRDRSIR
		     LVSGFLALAWDDLRSLCLFLYHRLRDFLLVIARTVEILGRSSLRGLQRGWEALKYLGN
		     LVQYWGSEIKKSAINLFDTIAIAVAEGTDRIIEIIQRIYRAICNIPVRIRQGFEAALL
		     "
     gene	     3885..4508
		     /gene="nef"
     CDS	     3885..4508
		     /gene="nef"
		     /codon_start="1"
		     /transl_table="1"
		     /product="nef protein"
		     /protein_id="AGU35818.1"
		     /db_xref="GI:534805122"
		     /translation="MGGKWSKSSPFGWPAVRERMRQTVPAAEGVGAASQDLDKRGALT
		     INNTPSNNEACAWLQAQEEEEEVGFPVRPQVPLRPMTFKGAFDLSFFLKEKGGLEGLI
		     YSRKRQEILDLWVYNTQGYFPDWQNYTPGPGVRYPLTFGWCFKLVPVDPKEVEEANEG
		     ENNCLLHPMSLHGMEDEEREVLKWVFDSRLAHRHVAREKHPEYYKDC"
BASE COUNT     1627 a	 823 c	 1133 g   1099 t
ORIGIN
       1 accctatttg gaaaggacca gccaaactac tctggaaagg tgaaggggca gtagtaatac 
      61 aagataacag tgacataaag gtagtaccaa ggaggaaagt aaaaatcatt aaggactatg 
     121 gaaaacagat ggcaggtgct gattgtgtgg caggtagaca ggatgaggat tagaacatgg 
     181 aatagtttag taaagcacca tatgtatgtg tcaaggagag ctcatggatg gttttacaga 
     241 catcattatg aaagcagaca tccaaaaata agttcagaag tacacatacc attaggggag 
     301 gctaggttag taataaaaac atattggggt ttgcaaacag gagaaagaga atggcacttg 
     361 ggtcatggag tctccataga atggagattg agaagatata gtacacaagt agaccctggc 
     421 ctggcagatc agctaattca tatgcattat tttgattgtt ttgcagactc tgccataaga 
     481 aaagccatat taggacacat agttattcct aggtgtgact atcaagcagg acacaataag 
     541 gtaggatctc tacaatactt ggcactgaca gcattgataa aaccaaaaaa gagaaagcca 
     601 cctctgccta gtgttaggaa attagtagag gatagatgga acaaccccca gaagaccagg 
     661 ggccgcagag ggaaccatac aatgaatgga cactagagat tctagaggaa ctcaagcagg 
     721 aagctgtcag acactttcct ataccatggc tccataactt aggacaatat atttatgaaa 
     781 cctatggaga tacttgggca ggagtcgaag ctataataaa aatactgcaa caactactgt 
     841 tcattcattt cagaattgga tgccaacata gcagaatagg cattttgaga cagagaagag 
     901 caagaaatgg agccaataga tcctaaacta gagccttgga accatccagg aagtaaacct 
     961 aaaactgctt gtaacaattg ttattgtaaa tgttgtagct accattgtct agtttgcttt 
    1021 cagacaaaag gcttaggcat ttcctatggc aggaagaagc ggagacagcg acgaagggct 
    1081 cctccaagca gtgaggatca tcaaaatcct atatcaaagc agtaagtata tgtaatgtca 
    1141 agtttaatag aaaaagtaga ttatagagta ggaatagcag cattaataat agcattactt 
    1201 atagcaatag ttgtgtggat catagtatat atagaatata ggaaattgtt aagacaaagg 
    1261 aaaatagact ggttagttga aagaattagg gaaagagcag aagacagtgg caatgagagt 
    1321 gagggggata ttgaggagtt ggcaaccatg ggggatatgg ggcatcttag gcttttggat 
    1381 ggtgttgact tgtagtgtac tagggaactt gtgggtcaca gtctattatg gggtacctgt 
    1441 gtggaaagaa gcaaaaacta ctctattctg tgcatcagat gctaaagcat atgagagaga 
    1501 aatgcacaat gtctgggcta cacatgcctg tgtgcccaca gaccccaacc cacaagaact 
    1561 ggttttggaa aatgtaacag aaaattttaa catgtggaaa aatgacatgg tagatcagat 
    1621 gcatgaggat ataatcagtt tatgggatca aagcctaaaa ccatgtgtaa agctgactcc 
    1681 actctgtgtc actttagatt gtaaaaatag tactgaaaat attactgata gcaggaatat 
    1741 tacagataat ggagaaagga aaaattgctc ttttaatata accacagaaa taaaagataa 
    1801 gaaacagaac gtgtatgcac ttttttataa acttgatata gtaccacttc atgaggacaa 
    1861 cagttcctac tatagactaa taaattgtaa tacctcagcc ataacacaag cctgtccaaa 
    1921 ggtctctttt gacccaattc ctatacacta ttgtgcacca gctggttatg cgattctaaa 
    1981 gtgtaataat aagacattca atgggacagg accatgccat aatgtcagca cagtacaatg 
    2041 tacacatgga attaagccag tggtatcaac tcaactactg ttaaatggta gcctagcaga 
    2101 agaagagata ataattagat ctaaagatct gacagacaat gccaaaataa taatagtaca 
    2161 ccttaataag tctgtagaga ttaattgtac aagacccggc aacaatacaa gaaaaagtat 
    2221 aaggatagga ccaggacaaa cattctatgc accaaatgga ataataggaa acataagaaa 
    2281 agcacattgt aacattaagg gaaagcagtg gaatgaaact ttaataaagg taggggaaaa 
    2341 attagcagaa ctcttcccta ataaaataat aaagtttaat tcatcctcag gaggggatct 
    2401 agaaattaca acacatagct ttaattgtgg aggagaattt ttctattgcg atacatcagg 
    2461 attgtttaat ggcacataca atcctaatga tacaacaagt aattcaagct cacttaacaa 
    2521 catcacactc acactcccat gcaaaataaa gcaagttata aacatgtggc agggggtagg 
    2581 aaaagcgata tatgcccctc ccattgcagg aaacataaca tgtagatcaa atatcacagg 
    2641 actactattg ctacgtgatg gaggaactac aaatgacaca gaagagatat tcagacctgg 
    2701 aggaggagat atgagggaca attggagaag tgaattatat aaatacaaag tggtagaaat 
    2761 taagccattg ggagtagcac ccactaaggc aaaaaggaga gtggtggaga gagaaaaaag 
    2821 agcagtggga ataggagctg tactccttgg gttcttagga gcggcaggaa gcactatggg 
    2881 cgcggcgtca ataacgctga cggtacaggc cagacaactg ttgtctggta tagtgcaaca 
    2941 gcaaagcaat ttgctgaggg ctatagaggc gcaacagcat atgttgcaac tcacggtctg 
    3001 gggcattaag cagctccagg ctagagtcct ggccatagaa agatacctaa aggatcaaca 
    3061 gctcctagga atttggggct gctctggaaa actcatctgc accacttctg tgccttggaa 
    3121 tgacagttgg agtcataata aatctctaca agatatttgg gataacatga cctggatgca 
    3181 gtgggataaa gaaattaata attacacaag cacaatatac aggttacttg aggaatcaca 
    3241 aaaccagcag gaaaaaaatg aacaagattt attagcattg gacagttggc aaaatctgtg 
    3301 gaattggttc agcatatcaa aatggctgtg gtatataaaa atattcataa tgatagtagg 
    3361 aggcttgata ggtttaagga taatttttgc tgtgctttct atagtgaata gagttaggca 
    3421 gggatactca cctttgtcgt ttcagaccct taccccaagc ccgaggggac ccgacaggct 
    3481 cggaagaatc gaagaagaag gtggagagca agacagagac agatccattc gattagtgag 
    3541 cggattctta gcacttgcct gggacgacct gcggagcctg tgcctcttcc tctaccaccg 
    3601 attgagagac tttctattgg tgatagcgag aacggtggaa attctgggac gcagcagtct 
    3661 caggggacta cagagggggt gggaagccct taaatatctg ggaaaccttg tgcagtattg 
    3721 gggttcagag ataaaaaaga gtgctattaa tctatttgat accatagcca tagcagtagc 
    3781 tgagggaaca gataggatta tagaaataat acaaagaatt tatagagcta tctgcaacat 
    3841 acctgtgaga ataagacagg gctttgaagc agctttgcta taaaatggga ggcaagtggt 
    3901 caaaaagcag cccatttgga tggcctgctg taagagagag aatgaggcaa actgtgccag 
    3961 cagcagaggg agtcggagca gcatctcaag acttagataa acgtggagca cttaccatca 
    4021 acaacacacc cagcaataat gaggcttgtg cctggctgca agcacaagag gaggaagaag 
    4081 aagtaggctt tccagtcaga cctcaggtgc ctttaagacc aatgactttt aagggagcat 
    4141 ttgatctcag cttcttttta aaagaaaagg ggggactgga agggttaatt tactctagga 
    4201 aaaggcaaga aatccttgat ttgtgggtct ataacacaca aggctatttc cctgattggc 
    4261 aaaactacac accgggacca ggggtcagat atccactgac ctttggatgg tgcttcaagc 
    4321 tagtaccagt tgaccccaag gaggtagaag aggccaacga aggagaaaac aactgtttgc 
    4381 tacaccctat gagcctacat ggaatggagg acgaagaaag agaagtatta aagtgggtgt 
    4441 ttgacagtcg cctagcacac agacacgtgg cccgcgagaa acatccggag tattacaaag 
    4501 actgctgaca cagaagggac tttccgctgg gactttccac cggggcgttc caggaggagg 
    4561 ggtctgggcg ggactaggga gtggccaacc ctcagatgct gcatataagc agctgctttt 
    4621 cgcctgtact gggtctctct aggtagacca gatctgagcc tgggagctct ctggccttct 
    4681 ag
//
last modified: Tue May 31 10:56 2022


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