{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T12:00:31Z","timestamp":1781784031886,"version":"3.54.5"},"reference-count":77,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2014,1,23]],"date-time":"2014-01-23T00:00:00Z","timestamp":1390435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0085452","type":"journal-article","created":{"date-parts":[[2014,1,23]],"date-time":"2014-01-23T23:28:00Z","timestamp":1390519680000},"page":"e85452","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":25,"title":["Molecular and Genetic Characterization of Natural HIV-1 Tat Exon-1 Variants from North India and Their Functional Implications"],"prefix":"10.1371","volume":"9","author":[{"given":"Larance","family":"Ronsard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sneh","family":"Lata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyotsna","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vishnampettai G.","family":"Ramachandran","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shukla","family":"Das","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akhil C.","family":"Banerjea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,1,23]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"2817","DOI":"10.1128\/JVI.62.8.2817-2822.1988","article-title":"Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication","volume":"62","author":"JP Dougherty","year":"1988","journal-title":"J Virol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/373123a0","article-title":"Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection","volume":"373","author":"DD Ho","year":"1995","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1128\/JVI.74.3.1234-1240.2000","article-title":"High rate of recombination throughout the human immunodeficiency virus type 1 genome","volume":"74","author":"AE Jetzt","year":"2000","journal-title":"J Virol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/nm.2016","article-title":"A new human immunodeficiency virus derived from gorillas","volume":"15","author":"JC Plantier","year":"2009","journal-title":"Nat Med"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 nomenclature proposal","volume":"288","author":"DL Robertson","year":"2000","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"W13","DOI":"10.1097\/01.aids.0000247564.73009.bc","article-title":"Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004","volume":"20","author":"J Hemelaar","year":"2006","journal-title":"AIDS"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1099\/0022-1317-42-1-1","article-title":"Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses","volume":"42","author":"JM Coffin","year":"1979","journal-title":"J Gen Virol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0092-8674(82)90011-3","article-title":"Retroviral DNA H structures: displacement-assimilation model of recombination","volume":"30","author":"RP Junghans","year":"1982","journal-title":"Cell"},{"key":"ref9","unstructured":"HIV Databases website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/CRFs\/CRFs.html\" xlink:type=\"simple\">www.hiv.lanl.gov\/content\/sequence\/HIV\/CRFs\/CRFs.html<\/ext-link>. Accessed 2011 December 10."},{"key":"ref10","doi-asserted-by":"crossref","first-page":"10209","DOI":"10.1128\/JVI.00872-07","article-title":"Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications","volume":"81","author":"L Buonaguro","year":"2007","journal-title":"J Virol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1002\/jmv.20572","article-title":"Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form 02_AG (CRF02_AG) has a higher in vitro replicative capacity than its parental subtypes A and G","volume":"78","author":"FA Konings","year":"2006","journal-title":"J Med Virol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1007\/s12038-008-0070-3","article-title":"HIV infection in India: epidemiology, molecular epidemiology and pathogenesis","volume":"33","author":"S Lakhashe","year":"2008","journal-title":"J Biosci"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1038\/313277a0","article-title":"Complete nucleotide sequence of the AIDS virus, HTLV-III","volume":"313","author":"L Ratner","year":"1985","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1016\/0092-8674(87)90247-9","article-title":"Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein","volume":"48","author":"MA Muesing","year":"1987","journal-title":"Cell"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2677","DOI":"10.1128\/JVI.68.4.2677-2682.1994","article-title":"The human immunodeficiency virus type 1 Tat protein transactivates tumor necrosis factor beta gene expression through a TAR-like structure","volume":"68","author":"L Buonaguro","year":"1994","journal-title":"J Virol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/0092-8674(89)90290-0","article-title":"HIV-1 Tat protein increases transcriptional initiation and stabilizes elongation","volume":"59","author":"MF Laspia","year":"1989","journal-title":"Cell"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"8602","DOI":"10.1128\/JVI.77.15.8602-8606.2003","article-title":"A naturally occurring substitution in human immunodeficiency virus Tat increases expression of the viral genome","volume":"77","author":"SM Reza","year":"2003","journal-title":"J Virol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"11030","DOI":"10.1073\/pnas.0404206101","article-title":"Prospects for inferring very large phylogenies by using the neighbor-joining method","volume":"101","author":"K Tamura","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"W654","DOI":"10.1093\/nar\/gkh419","article-title":"A web-based genotyping resource for viral sequences","volume":"32","author":"M Rozanov","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"KS Lole","year":"1999","journal-title":"J Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1016\/j.micinf.2005.06.003","article-title":"Decoding Tat: the biology of HIV Tat posttranslational modifications","volume":"7","author":"C Hetzer","year":"2005","journal-title":"Microbes Infect"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1742-4690-5-40","article-title":"Lysine methylation of HIV-1 Tat regulates transcriptional activity of the viral LTR","volume":"5","author":"R Van Duyne","year":"2008","journal-title":"Retrovirology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1631\/jzus.2005.B0668","article-title":"Extracellular HIV Tat and Tat cysteine rich peptide increase CCR5 expression in monocytes","volume":"6","author":"L Zheng","year":"2005","journal-title":"J Zhejiang Univ Sci B"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1006\/viro.1997.8786","article-title":"Determination of the minimal amount of Tat activity required for human immunodeficiency virus type 1 replication","volume":"237","author":"K Verhoef","year":"1997","journal-title":"Virology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1101\/gad.5.2.201","article-title":"Analysis of arginine-rich peptides from the HIV Tat protein reveals unusual features of RNA-protein recognition","volume":"5","author":"BJ Calnan","year":"1991","journal-title":"Genes Dev"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/S1097-2765(02)00483-5","article-title":"Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain","volume":"9","author":"S Mujtaba","year":"2002","journal-title":"Mol Cell"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4247","DOI":"10.1073\/pnas.95.8.4247","article-title":"A novel glutamine-RNA interaction identified by screening libraries in mammalian cells","volume":"95","author":"R Tan","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"48197","DOI":"10.1074\/jbc.M406195200","article-title":"The glutamine-rich region of the HIV-1 Tat protein is involved in T-cell apoptosis","volume":"279","author":"GR Campbell","year":"2004","journal-title":"J Biol Chem"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1006\/viro.1995.0014","article-title":"HIV-1 Tat directly interacts with the interferon-induced, double-stranded RNA-dependent kinase, PKR","volume":"213","author":"NA McMillan","year":"1995","journal-title":"Virology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/1743-422X-2-17","article-title":"Phosphorylation of HIV Tat by PKR increases interaction with TAR RNA and enhances transcription","volume":"2","author":"L Endo-Munoz","year":"2005","journal-title":"Virol J"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1006\/jmbi.1999.3310","article-title":"Sequence and structure-based prediction of eukaryotic protein phosphorylation sites","volume":"294","author":"N Blom","year":"1999","journal-title":"J Mol Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"W433","DOI":"10.1093\/nar\/gkm352","article-title":"MyHits: improvements to an interactive resource for analyzing protein sequences","volume":"35","author":"M Pagni","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1038\/ncb1704","article-title":"The NHL-domain protein Wech is crucial for the integrin-cytoskeleton link","volume":"10","author":"B Loer","year":"2008","journal-title":"Nat Cell Biol"},{"key":"ref36","unstructured":"Korber B (2000) HIV Signature and Sequence Variation Analysis: Computational Analysis of HIV Molecular Sequences: Edited by Allen G. Rodrigo and Gerald H. Learn; Dordrecht; Netherlands: Kluwer Academic Publishers: Chapter 4; pages 55\u201372."},{"key":"ref37","article-title":"Mechanism of apoptotic induction in human breast cancer cell, MCF-7, by an analog of curcumin in comparison with curcumin - An in vitro and in silico approach","author":"K Mohankumar","year":"2013","journal-title":"Chem Biol Interact"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"10479","DOI":"10.1128\/JVI.75.21.10479-10487.2001","article-title":"Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences","volume":"75","author":"R Shankarappa","year":"2001","journal-title":"J Virol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1097\/01.aids.0000180795.49016.89","article-title":"Identification of unique B\/C recombinant strains of HIV-1 in the southern state of Karnataka, India","volume":"19","author":"NB Siddappa","year":"2005","journal-title":"AIDS"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1089\/aid.2005.21.152","article-title":"Subtype B and subtype C HIV type 1 recombinants in the northeastern state of Manipur, India","volume":"21","author":"SP Tripathy","year":"2005","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1086\/339547","article-title":"Human immunodeficiency virus superinfection and recombination: current state of knowledge and potential clinical consequences","volume":"34","author":"JT Blackard","year":"2002","journal-title":"Clin Infect Dis"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1742-4690-3-14","article-title":"Higher transactivation activity associated with LTR and Tat elements from HIV-1 BF intersubtype recombinant variants","volume":"3","author":"G Turk","year":"2006","journal-title":"Retrovirology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1742-4690-7-25","article-title":"The role of recombination in the emergence of a complex and dynamic HIV epidemic","volume":"7","author":"M Zhang","year":"2010","journal-title":"Retrovirology"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e59283","DOI":"10.1371\/journal.pone.0059283","article-title":"Genetic characterization of natural variants of Vpu from HIV-1 infected individuals from Northern India and their impact on virus release and cell death","volume":"8","author":"S Verma","year":"2013","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e82128","DOI":"10.1371\/journal.pone.0082128","article-title":"Effect on HIV-1 Gene Expression, Tat-Vpr Interaction and Cell Apoptosis by Natural Variants of HIV-1 Tat Exon 1 and Vpr from Northern India","volume":"8","author":"S Lata","year":"2013","journal-title":"PLoS One"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"769","DOI":"10.4103\/0971-5916.92624","article-title":"Genetic architecture of HIV-1 genes circulating in north India &amp; their functional implications","volume":"134","author":"U Neogi","year":"2011","journal-title":"Indian J Med Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.virusres.2009.10.024","article-title":"Molecular characterization of tat gene and long terminal repeat region of human immunodeficiency virus type-1 detected among the injecting drug users (IDUs) of Manipur, India: identification of BC recombinants","volume":"147","author":"R Mullick","year":"2010","journal-title":"Virus Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.virol.2008.12.025","article-title":"High replication fitness and transmission efficiency of HIV-1 subtype C from India: Implications for subtype C predominance","volume":"385","author":"MA Rodriguez","year":"2009","journal-title":"Virology"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.1097\/QAD.0b013e3282f56114","article-title":"Functional analysis of HIV-1 subtypes B and C HIV-1 Tat exons and RGD\/QGD motifs with respect to Tat-mediated transactivation and apoptosis","volume":"22","author":"V Sood","year":"2008","journal-title":"AIDS"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1097\/QAD.0b013e32831c8b08","article-title":"C-terminal half of HIV-1 Vif C possesses major determinant for APOBEC3G degradation","volume":"23","author":"N Gupta","year":"2009","journal-title":"AIDS"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1006\/abbi.1999.1206","article-title":"Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA","volume":"365","author":"TM Rana","year":"1999","journal-title":"Arch Biochem Biophys"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"28837","DOI":"10.1074\/jbc.274.41.28837","article-title":"Multifaceted activities of the HIV-1 transactivator of transcription, Tat","volume":"274","author":"KT Jeang","year":"1999","journal-title":"J Biol Chem"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/nature09131","article-title":"Crystal structure of HIV-1 Tat complexed with human P-TEFb","volume":"465","author":"TH Tahirov","year":"2010","journal-title":"Nature"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1101\/gad.4.8.1365","article-title":"A bulge structure in HIV-1 TAR RNA is required for Tat binding and Tat-mediated trans-activation","volume":"4","author":"S Roy","year":"1990","journal-title":"Genes Dev"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"9180","DOI":"10.1128\/JVI.79.14.9180-9191.2005","article-title":"Regulation of human immunodeficiency virus type 1 gene expression by clade-specific Tat proteins","volume":"79","author":"Y Desfosses","year":"2005","journal-title":"J Virol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"e17185","DOI":"10.1371\/journal.pone.0017185","article-title":"T-cell immune responses against Env from CRF12_BF and subtype B HIV-1 show high clade-specificity that can be overridden by multiclade immunizations","volume":"6","author":"DC Monaco","year":"2011","journal-title":"PLoS One"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"9280","DOI":"10.1074\/jbc.M110.208884","article-title":"Regulation of Tat acetylation and transactivation activity by the microtubule-associated deacetylase HDAC6","volume":"286","author":"L Huo","year":"2011","journal-title":"J Biol Chem"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nature07352","article-title":"Challenges in the development of an HIV-1 vaccine","volume":"455","author":"DH Barouch","year":"2008","journal-title":"Nature"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1086\/508748","article-title":"Randomized, double-blind, placebo-controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV-1 vaccine among injection drug users in Bangkok, Thailand","volume":"194","author":"P Pitisuttithum","year":"2006","journal-title":"J Infect Dis"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1016\/S0140-6736(08)61592-5","article-title":"HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case-cohort analysis","volume":"372","author":"MJ McElrath","year":"2008","journal-title":"Lancet"},{"key":"ref61","first-page":"123605","article-title":"Impact of Tat Genetic Variation on HIV-1 Disease","volume":"2012","author":"L Li","year":"2012","journal-title":"Adv Virol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"5528","DOI":"10.1128\/JVI.71.7.5528-5539.1997","article-title":"Recognition of prominent viral epitopes induced by immunization with human immunodeficiency virus type 1 regulatory genes","volume":"71","author":"J Hinkula","year":"1997","journal-title":"J Virol"},{"key":"ref63","first-page":"208","article-title":"Block of HIV-1 infection by a combination of antisense tat RNA and TAR decoys: a strategy for control of HIV-1","volume":"1","author":"HK Chang","year":"1994","journal-title":"Gene Ther"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"197","DOI":"10.4049\/jimmunol.168.1.197","article-title":"Native HIV-1 Tat protein targets monocyte-derived dendritic cells and enhances their maturation, function, and antigen-specific T cell responses","volume":"168","author":"E Fanales-Belasio","year":"2002","journal-title":"J Immunol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"3838","DOI":"10.4049\/jimmunol.173.6.3838","article-title":"HIV-1 tat protein modulates the generation of cytotoxic T cell epitopes by modifying proteasome composition and enzymatic activity","volume":"173","author":"R Gavioli","year":"2004","journal-title":"J Immunol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1666","DOI":"10.4049\/jimmunol.159.4.1666","article-title":"Introduction of soluble proteins into the MHC class I pathway by conjugation to an HIV tat peptide","volume":"159","author":"DT Kim","year":"1997","journal-title":"J Immunol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"8952","DOI":"10.1128\/JVI.72.11.8952-8960.1998","article-title":"Tat protein induces human immunodeficiency virus type 1 (HIV-1) coreceptors and promotes infection with both macrophage-tropic and T-lymphotropic HIV-1 strains","volume":"72","author":"L Huang","year":"1998","journal-title":"J Virol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1038\/345084a0","article-title":"Tat protein of HIV-1 stimulates growth of cells derived from Kaposi&apos;s sarcoma lesions of AIDS patients","volume":"345","author":"B Ensoli","year":"1990","journal-title":"Nature"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1038\/nm0996-960","article-title":"HIV-1 Tat protein as a potential AIDS vaccine","volume":"2","author":"G Goldstein","year":"1996","journal-title":"Nat Med"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"2207","DOI":"10.1097\/QAD.0b013e32831392d4","article-title":"The therapeutic phase I trial of the recombinant native HIV-1 Tat protein","volume":"22","author":"B Ensoli","year":"2008","journal-title":"AIDS"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"3306","DOI":"10.1016\/j.vaccine.2009.01.090","article-title":"Phase I therapeutic trial of the HIV-1 Tat protein and long term follow-up","volume":"27","author":"O Longo","year":"2009","journal-title":"Vaccine"},{"key":"ref72","unstructured":"DNA Data Bank of Japan website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/clustalw.ddbj.nig.ac.jp\/\" xlink:type=\"simple\">http:\/\/clustalw.ddbj.nig.ac.jp\/<\/ext-link>. Accessed 2012 February 14."},{"key":"ref73","unstructured":"NCBI Genotyping website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/projects\/genotyping\/formpage.cgi\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/projects\/genotyping\/formpage.cgi<\/ext-link>. Accessed 2012 February 14."},{"key":"ref74","unstructured":"REGA HIV-1 Subtyping Tool website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/dbpartners.stanford.edu\/RegaSubtyping\/\" xlink:type=\"simple\">http:\/\/dbpartners.stanford.edu\/RegaSubtyping\/<\/ext-link>. Accessed 2012 February 14."},{"key":"ref75","unstructured":"HIV Database Tools website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.hiv.lanl.gov\/content\/sequence\/SNAP\/SNAP.html\" xlink:type=\"simple\">http:\/\/www.hiv.lanl.gov\/content\/sequence\/SNAP\/SNAP.html<\/ext-link>. Accessed 2012 February 14."},{"key":"ref76","unstructured":"Motif scan website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/myhits.isb-sib.ch\/cgi-bin\/motif_scan\" xlink:type=\"simple\">http:\/\/myhits.isb-sib.ch\/cgi-bin\/motif_scan<\/ext-link>. Accessed 2012 March 10."},{"key":"ref77","unstructured":"NetPhos2.0 Server website. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.cbs.dtu.dk\/services\/NetPhos\/\" xlink:type=\"simple\">http:\/\/www.cbs.dtu.dk\/services\/NetPhos\/<\/ext-link>. Accessed 2011 December 10."}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0085452","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T00:33:19Z","timestamp":1688949199000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0085452"}},"subtitle":[],"editor":[{"given":"Shilpa J.","family":"Buch","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,1,23]]},"references-count":77,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,1,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0085452","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,23]]}}}