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Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.hiv.lanl.gov\/content\/index\" xlink:type=\"simple\">http:\/\/www.hiv.lanl.gov\/content\/index<\/ext-link>. Accessed 2013 Mar 22."},{"key":"ref6","unstructured":"Tanzania Commission for AIDS (TACAIDS), Zanzibar AIDS Commission (ZAC), National Bureau of Statistics (NBS), Office of the Chief Government Statistician and Macro International Inc (2007) Tanzania HIV\/AIDS and Malaria Indicator Survey. Dar es Salaam, Tanzania."},{"key":"ref7","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1111\/j.1600-0463.2008.00996.x","article-title":"Evolution of human immunodeficiency virus type 1 serotypes in northern Tanzania: a retrospective study","volume":"116","author":"BM Nyombi","year":"2008","journal-title":"APMIS"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1089\/aid.2007.0311","article-title":"Diversity of human immunodeficiency virus type 1 subtypes in Kagera and Kilimanjaro regions, Tanzania","volume":"24","author":"BM Nyombi","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1089\/aid.2006.22.599","article-title":"Frequency of HIV type 1 dual infection and HIV diversity: analysis of low- and high-risk populations in Mbeya Region, Tanzania","volume":"22","author":"K-H Herbinger","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1177\/135965350801302S08","article-title":"Surveillance of transmitted HIV drug resistance among women attending antenatal clinics in Dar es Salaam, Tanzania","volume":"13","author":"GR Somi","year":"2008","journal-title":"Antivir Ther"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e47605","DOI":"10.1371\/journal.pone.0047605","article-title":"HIV-1 subtypes and recombinants in northern Tanzania: distribution of viral quasispecies","volume":"7","author":"IE Kiwelu","year":"2012","journal-title":"PLoS ONE"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1089\/aid.2011.0024","article-title":"HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda","volume":"28","author":"D Ssemwanga","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1089\/aid.2011.0089","article-title":"HIV type 1 subtype surveillance in central Kenya","volume":"28","author":"S Kageha","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e42557","DOI":"10.1371\/journal.pone.0042557","article-title":"Molecular and phylogeographic analysis of human immuno-deficiency virus type 1 strains infecting treatment-naive patients from Kigali, Rwanda","volume":"7","author":"J Rusine","year":"2012","journal-title":"PLoS ONE"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1097\/01.COH.0000232344.23533.be","article-title":"Viral diversity as a challenge to HIV-1 vaccine development","volume":"1","author":"JK Carr","year":"2006","journal-title":"Curr Opin in HIV and AIDS"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1056\/NEJMc086373","article-title":"The challenge of HIV-1 subtype diversity","volume":"359","author":"BS Taylor","year":"2008","journal-title":"N Engl J Med"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"i97","DOI":"10.1136\/sti.78.suppl_1.i97","article-title":"Sociodemographic context of the AIDS epidemic in a rural area in Tanzania with a focus on people&apos;s mobility and marriage","volume":"78","author":"JT Boerma","year":"2002","journal-title":"Sex Transm Infect"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1097\/QAI.0b013e31815a571a","article-title":"HIV prevalence and incidence in rural Tanzania: results from 10 years of follow-up in an open-cohort study","volume":"46","author":"M Wambura","year":"2007","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref19","first-page":"359","article-title":"Susceptibility of HIV-1 isolates to zidovudine: correlation between widely applicable culture test and PCR analysis","volume":"5","author":"M Jung","year":"1992","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1097\/00002030-199102000-00002","article-title":"Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes","volume":"5","author":"BA Larder","year":"1991","journal-title":"AIDS"},{"key":"ref21","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":"ref22","doi-asserted-by":"crossref","first-page":"3963","DOI":"10.1128\/JCM.43.8.3963-3970.2005","article-title":"Model for assessment of proficiency of Human Immunodeficiency Virus type 1 sequencing-based genotypic antiretroviral assays","volume":"43","author":"DD Huang","year":"2005","journal-title":"J Clin Microbiol"},{"key":"ref23","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":"ref24","unstructured":"Stanford University (n.d.) HIV drug resistance database. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/hivdb.stanford.edu\/\" xlink:type=\"simple\">http:\/\/hivdb.stanford.edu\/<\/ext-link>. Accessed 2012 Dec 21."},{"key":"ref25","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/molbev\/msp259","article-title":"SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building","volume":"27","author":"M Gouy","year":"2010","journal-title":"Mol Biol Evol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the human-ape splitting by a molecular clock of mitochondrial DNA","volume":"22","author":"M Hasegawa","year":"1985","journal-title":"J Mol Evol"},{"key":"ref27","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence limits on phylogenies: an approach using the bootstrap","volume":"39","author":"J Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1089\/08892220360473970","article-title":"HIV type 1 subtypes among bar and hotel workers in Moshi, Tanzania","volume":"19","author":"IE Kiwelu","year":"2003","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1097\/QCO.0b013e32834ef5af","article-title":"HIV-1 superinfection","volume":"25","author":"L Waters","year":"2012","journal-title":"Curr Opin Infect Dis"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e7702","DOI":"10.1371\/journal.pone.0007702","article-title":"Inaccurate diagnosis of HIV-1 group M and O is a key challenge for ongoing universal access to antiretroviral treatment and HIV prevention in Cameroon","volume":"4","author":"AF Aghokeng","year":"2009","journal-title":"PLoS ONE"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1758-2652-13-4","article-title":"Impact of HIV-1 viral subtype on disease progression and response to antiretroviral therapy","volume":"13","author":"PJ Easterbrook","year":"2010","journal-title":"J Int AIDS Soc"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1097\/COH.0b013e32832f129e","article-title":"The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility","volume":"4","author":"B Korber","year":"2009","journal-title":"Curr Opin in HIV and AIDS"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1086\/527416","article-title":"Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection","volume":"197","author":"N Kiwanuka","year":"2008","journal-title":"J Infect Dis"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1097\/00002030-200102160-00001","article-title":"Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort","volume":"15","author":"P Kaleebu","year":"2001","journal-title":"AIDS"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0166-0934(01)00272-5","article-title":"HIV-1 subtyping using phylogenetic analysis of pol gene sequences","volume":"94","author":"C Pasquier","year":"2001","journal-title":"J Virol Methods"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0081848","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,8]],"date-time":"2023-07-08T22:46:34Z","timestamp":1688856394000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0081848"}},"subtitle":[],"editor":[{"given":"Jianqing","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,12,11]]},"references-count":36,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2013,12,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0081848","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,11]]}}}