{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T03:51:46Z","timestamp":1791085906518,"version":"4.1.0"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2012,3,28]],"date-time":"2012-03-28T00:00:00Z","timestamp":1332892800000},"content-version":"unspecified","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.0033579","type":"journal-article","created":{"date-parts":[[2012,3,28]],"date-time":"2012-03-28T21:15:02Z","timestamp":1332969302000},"page":"e33579","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["The Origin and Evolutionary History of HIV-1 Subtype C in Senegal"],"prefix":"10.1371","volume":"7","author":[{"given":"Matthieu","family":"Jung","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nafissatou","family":"Leye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Vidal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denis","family":"Fargette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Halimatou","family":"Diop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Coumba","family":"Toure Kane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Gascuel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martine","family":"Peeters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,3,28]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S1473-3099(02)00343-2","article-title":"Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy.","volume":"2","author":"MM Thomson","year":"2002","journal-title":"Lancet Infect Dis"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1525","DOI":"10.1111\/j.1469-0691.2010.03300.x","article-title":"Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays.","volume":"16","author":"M Peeters","year":"2010","journal-title":"Clin Microbiol Infect"},{"key":"ref3","first-page":"9","article-title":"Current progress in the development of a prophylactic vaccine for HIV-1.","volume":"5","author":"LJ Gamble","year":"2010","journal-title":"Drug Des Devel Ther"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S1473-3099(10)70186-9","article-title":"Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease.","volume":"11","author":"DM Tebit","year":"2011","journal-title":"Lancet Infect Dis"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"10498","DOI":"10.1128\/JVI.74.22.10498-10507.2000","article-title":"Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa.","volume":"74","author":"N Vidal","year":"2000","journal-title":"J Virol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/35074179","article-title":"Human immunodeficiency virus. Phylogeny and the origin of HIV-1.","volume":"410","author":"A Rambaut","year":"2001","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature07390","article-title":"Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.","volume":"455","author":"M Worobey","year":"2008","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1097\/QAD.0b013e328342ff93","article-title":"Global trends in molecular epidemiology of HIV-1 during 2000\u20132007.","volume":"25","author":"J Hemelaar","year":"2011","journal-title":"AIDS"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1016\/S0140-6736(85)92556-5","article-title":"Serological evidence for virus related to simian T-lymphotropic retrovirus III in residents of west Africa.","volume":"2","author":"F Barin","year":"1985","journal-title":"Lancet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1089\/aid.2007.0037","article-title":"Twenty years of prospective molecular epidemiology in Senegal: changes in HIV diversity.","volume":"23","author":"DJ Hamel","year":"2007","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref11","article-title":"UNAIDS website."},{"key":"ref12","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1089\/088922200309025","article-title":"Identification of all HIV type 1 group M subtypes in Senegal, a country with low and stable seroprevalence.","volume":"16","author":"C Toure-Kane","year":"2000","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1089\/aid.2009.0142","article-title":"Low prevalence of HIV type 1 drug resistance mutations in untreated, recently infected patients from Burkina Faso, C\u00f4te d&apos;Ivoire, Senegal, Thailand, and Vietnam: the ANRS 12134 study.","volume":"25","author":"A Ayouba","year":"2009","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1089\/aid.2009.0295","article-title":"Antiretroviral drug resistance mutations in antiretroviral-naive patients from Senegal.","volume":"26","author":"H Diop-Ndiaye","year":"2010","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1097\/QAI.0b013e3181af70a4","article-title":"Surprisingly high prevalence of subtype C and specific HIV-1 subtype\/CRF distribution in men having sex with men in Senegal.","volume":"52","author":"HD Ndiaye","year":"2009","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref16","doi-asserted-by":"crossref","DOI":"10.1097\/01.aids.0000191497.00928.e4","article-title":"HIV-1 subtype C dissemination in southern Brazil.","volume":"19","author":"EA Soares","year":"2005","journal-title":"AIDS"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1097\/01.aids.0000194128.97640.07","article-title":"HIV infection and sexually transmitted infections among men who have sex with men in Senegal.","volume":"19","author":"AS Wade","year":"2005","journal-title":"AIDS"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.virol.2011.03.021","article-title":"Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning.","volume":"415","author":"MM Thomson","year":"2011","journal-title":"Virology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1097\/QAD.0b013e3283108f69","article-title":"On the origin of HIV-1 subtype C in South America.","volume":"22","author":"R Fontella","year":"2008","journal-title":"AIDS"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1097\/QAD.0b013e328315e0aa","article-title":"Origin and evolutionary history of HIV-1 subtype C in Brazil.","volume":"22","author":"G Bello","year":"2008","journal-title":"AIDS"},{"issue":"2","key":"ref21","doi-asserted-by":"crossref","first-page":"e9311","DOI":"10.1371\/journal.pone.0009311","article-title":"The HIV-1 subtype C epidemic in South America is linked to the United Kingdom.","volume":"5","author":"T de Oliveira","year":"2010","journal-title":"PLoS One"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1099\/vir.0.028951-0","article-title":"High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America.","volume":"92","author":"NM V\u00e9ras","year":"2011","journal-title":"J Gen Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1097\/00002030-199309000-00017","article-title":"Temporary expatriation is related to HIV-1 infection in rural Senegal.","volume":"9","author":"F Kane","year":"1993","journal-title":"AIDS"},{"key":"ref24","first-page":"S33","article-title":"Virology of HIV-1 and HIV-2: implications for Africa.","volume":"11","author":"PJ Kanki","year":"1997","journal-title":"AIDS"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1086\/314557","article-title":"Human immunodeficiency virus type 1 subtypes differ in disease progression.","volume":"179","author":"PJ Kanki","year":"1999","journal-title":"J Infect Dis"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1097\/QAD.0b013e32833999e1","article-title":"Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia.","volume":"24","author":"DC Tully","year":"2010","journal-title":"AIDS"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.1097\/QAD.0b013e3283320ef3","article-title":"Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe.","volume":"23","author":"SC Dalai","year":"2009","journal-title":"AIDS"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"10501","DOI":"10.1128\/JVI.78.19.10501-10506.2004","article-title":"Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.","volume":"78","author":"SA Travers","year":"2004","journal-title":"J Virol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1097\/COH.0b013e32833a0b86","article-title":"Sexual risk behaviour for transmission of HIV in men who have sex with men: recent findings and potential interventions.","volume":"5","author":"LM McDaid","year":"2010","journal-title":"Curr Opin HIV AIDS"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"5592","DOI":"10.1128\/JVI.02051-08","article-title":"CCR5-and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic,","volume":"83","author":"A Abraha","year":"2009","journal-title":"J Virol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1128\/JVI.77.2.1021-1038.2003","article-title":"Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes B and C.","volume":"77","author":"SC Ball","year":"2003","journal-title":"J Virol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1629","DOI":"10.1097\/01.aids.0000131392.68597.34","article-title":"Preferential in-utero transmission of HIV-1 subtype C as compared to HIV-1 subtype A or D.","volume":"18","author":"B Renjifo","year":"2004","journal-title":"AIDS"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1086\/431514","article-title":"Subtype C is associated with increased vaginal shedding of HIV-1.","volume":"192","author":"GC John-Stewart","year":"2005","journal-title":"J Infect Dis"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1758-2652-12-11","article-title":"Differences in resistance mutations among HIV-1 non-subtype B infections: A systematic review of evidence (1996\u20132008).","volume":"12","author":"JL Martinez-Cajas","year":"2009","journal-title":"J Int AIDS Soc"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/j.1574-695X.2005.00011.x","article-title":"Genotypic drug resistance interpretation algorithms display high levels of discordance when applied to non-B strains from HIV-1 naive and treated patients.","volume":"46","author":"L Vergne","year":"2006","journal-title":"FEMS Immunol Med Microbiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1128\/AAC.50.2.694-701.2006","article-title":"Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent.","volume":"50","author":"J Snoeck","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"4393","DOI":"10.1128\/JVI.73.5.4393-4403.1999","article-title":"Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya.","volume":"73","author":"JR Neilson","year":"1999","journal-title":"J Virol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/135965350801302S03","article-title":"The World Health Organization&apos;s global strategy for prevention and assessment of HIV drug resistance.","volume":"13","author":"DE Bennett","year":"2008","journal-title":"Antivir Ther"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences.","volume":"21","author":"T de Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/nar\/gkp455","article-title":"Standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.","volume":"37","author":"LC Alcantara","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1177\/135965350601100511","article-title":"HIV-1 drug-resistance mutations among newly diagnosed patients before scaling-up programmes in Burkina Faso and Cameroon.","volume":"11","author":"L Vergne","year":"2006","journal-title":"Antivir Ther"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment.","volume":"33","author":"K Katoh","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref44","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":"ref45","doi-asserted-by":"crossref","first-page":"e4724","DOI":"10.1371\/journal.pone.0004724","article-title":"Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update.","author":"DE Bennett","year":"2009","journal-title":"PLoS One"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1093\/oxfordjournals.molbev.a003890","article-title":"Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1).","volume":"18","author":"D Posada","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.","volume":"59","author":"S Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1080\/10635150600755453","article-title":"Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.","volume":"55","author":"M Anisimova","year":"2006","journal-title":"Syst Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models.","volume":"19","author":"F Ronquist","year":"2003","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees.","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence.","volume":"4","author":"AJ Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1093\/molbev\/msn090","article-title":"Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.","volume":"25","author":"VN Minin","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"6089","DOI":"10.1128\/JVI.79.10.6089-6101.2005","article-title":"Biologic and genetic characterization of a panel of 60 human immunodeficiency virus type 1 isolates, representing clades A, B, C, D, CRF01_AE, and CRF02_AG, for the development and assessment of candidate vaccines.","volume":"79","author":"BK Brown","year":"2005","journal-title":"J Virol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"S31","DOI":"10.1097\/00002030-200317003-00005","article-title":"Low rate of genotypic HIV-1 drug-resistant strains in the Senegalese government initiative of access to antiretroviral therapy.","volume":"17","author":"L Vergne","year":"2003","journal-title":"AIDS"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"3919","DOI":"10.1128\/JCM.38.11.3919-3925.2000","article-title":"Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-na\u00efve patients.","volume":"38","author":"L Vergne","year":"2000","journal-title":"J Clin Microbiol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0033579","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,22]],"date-time":"2024-04-22T09:13:22Z","timestamp":1713777202000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0033579"}},"subtitle":[],"editor":[{"given":"Chiyu","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,3,28]]},"references-count":55,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2012,3,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0033579","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,3,28]]}}}