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Accessed: January 12, 2017. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/en\/regionscountries\/countries\/southafrica\" xlink:type=\"simple\">http:\/\/www.unaids.org\/en\/regionscountries\/countries\/southafrica<\/ext-link>."},{"key":"ref2","unstructured":"SANAC. The South African National AIDS Council. HIV Statistics. 2016. Accessed: January 14, 2017. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ivizard.org\/sanac\/\" xlink:type=\"simple\">http:\/\/ivizard.org\/sanac\/<\/ext-link>."},{"key":"ref3","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1186\/1471-2458-12-231","article-title":"HIV prevalence among high school learners\u2014opportunities for schools-based HIV testing programmes and sexual reproductive health services","volume":"12","author":"AB Kharsany","year":"2012","journal-title":"BMC Public Health"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1742-6405-10-30","article-title":"Women and HIV in sub-Saharan Africa","volume":"10","author":"G Ramjee","year":"2013","journal-title":"AIDS Res Ther"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1089\/aid.2014.0110","article-title":"HIV infection in high school students in rural South Africa: role of transmissions among students","volume":"30","author":"AB Kharsany","year":"2014","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1097\/COH.0000000000000040","article-title":"Molecular tools for studying HIV transmission in sexual networks","volume":"9","author":"MK Grabowski","year":"2014","journal-title":"Curr Opin HIV AIDS"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/molbev\/msw217","article-title":"Phylogenetic tools for generalized HIV-1 epidemics: findings from the PANGEA-HIV methods comparison","volume":"34","author":"O Ratmann","year":"2017","journal-title":"Mol Biol Evol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1097\/QAI.0000000000000271","article-title":"Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?","volume":"67","author":"AM Dennis","year":"2014","journal-title":"J Acquir Immune 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epidemics in rural Uganda: evidence from spatial clustering, phylogenetics, and egocentric transmission models","volume":"11","author":"MK Grabowski","year":"2014","journal-title":"PLoS Med"},{"key":"ref16","article-title":"Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases","author":"S Le Vu","year":"2017","journal-title":"Epidemics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e978","DOI":"10.1016\/S2214-109X(16)30253-4","article-title":"The effect of a conditional cash transfer on HIV incidence in young women in rural South Africa (HPTN 068): a phase 3, randomised controlled trial","volume":"4","author":"A Pettifor","year":"2016","journal-title":"Lancet Glob Health"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1093\/ije\/dys115","article-title":"Profile: Agincourt health and socio-demographic surveillance system","volume":"41","author":"K Kahn","year":"2012","journal-title":"Int J Epidemiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1080\/09540121.2012.750710","article-title":"Prevalence of HIV among those 15 and older in rural South Africa","volume":"25","author":"FX Gomez-Olive","year":"2013","journal-title":"AIDS Care"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"23514","DOI":"10.3402\/gha.v7.23514","article-title":"Migration and the epidemiological transition: insights from the Agincourt sub-district of northeast South Africa","volume":"7","author":"MA Collinson","year":"2014","journal-title":"Glob Health Action"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1159\/000331998","article-title":"The HIVdb system for HIV-1 genotypic resistance interpretation","volume":"55","author":"MW Tang","year":"2012","journal-title":"Intervirology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1007\/s10461-015-1270-0","article-title":"HPTN 068: A randomized control trial of a conditional cash transfer to reduce HIV infection in young women in South Africa-study design and baseline results","volume":"20","author":"A Pettifor","year":"2016","journal-title":"AIDS Behav"},{"key":"ref23","unstructured":"de Oliveira T, Deforche K, Cassol S, Rambaut A, Vandamme A-M. REGA HIV-1 subtyping tool 2014. Accessed: December 7, 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/dbpartners.stanford.edu:8080\/RegaSubtyping\/stanford-hiv\/typingtool\/\" xlink:type=\"simple\">http:\/\/dbpartners.stanford.edu:8080\/RegaSubtyping\/stanford-hiv\/typingtool\/<\/ext-link>."},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS One"},{"key":"ref25","unstructured":"HIV Sequence Database: Los Alamos National Laboratory; 2016. Accessed: December 7, 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html\" xlink:type=\"simple\">https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html<\/ext-link>."},{"key":"ref26","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":"ref27","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/bioinformatics\/16.6.562","article-title":"RDP: detection of recombination amongst aligned sequences","volume":"16","author":"D Martin","year":"2000","journal-title":"Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1007\/BF00182389","article-title":"Analyzing the mosaic structure of genes","volume":"34","author":"JM Smith","year":"1992","journal-title":"J Mol Evol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"13757","DOI":"10.1073\/pnas.241370698","article-title":"Evaluation of methods for detecting recombination from DNA sequences: computer simulations","volume":"98","author":"D Posada","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1089\/aid.2005.21.98","article-title":"A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints","volume":"21","author":"DP Martin","year":"2005","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/bioinformatics\/16.7.573","article-title":"Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences","volume":"16","author":"MJ Gibbs","year":"2000","journal-title":"Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and analysis of recombination patterns in virus genomes","volume":"1","author":"DP Martin","year":"2015","journal-title":"Virus Evol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref34","unstructured":"Rambaut A. FigTree v1.4.3: Molecular evolution, phylogenetics and epidemiology; 2007. updated October 4, 2016. Accessed: December 7, 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/\" xlink:type=\"simple\">http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/<\/ext-link>."},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1006000","DOI":"10.1371\/journal.ppat.1006000","article-title":"Social and Genetic Networks of HIV-1 Transmission in New York City","volume":"13","author":"JO Wertheim","year":"2017","journal-title":"PLoS Pathog"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1186\/1471-2105-14-317","article-title":"Automated analysis of phylogenetic clusters","volume":"14","author":"M Ragonnet-Cronin","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/infdis\/jit524","article-title":"The global transmission network of HIV-1","volume":"209","author":"JO Wertheim","year":"2014","journal-title":"J Infect Dis"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"I Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"AJ Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref40","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":"ref41","unstructured":"Rambaut A, Suchard MA, Xie D, Drummond AJ. Tracer v1.6 2014. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/\" xlink:type=\"simple\">http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/<\/ext-link>."},{"key":"ref42","year":"2016"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s12985-015-0244-1","article-title":"HIV-1 diversity in an antiretroviral treatment naive cohort from Bushbuckridge, Mpumalanga Province, South Africa","volume":"12","author":"PW Msimanga","year":"2015","journal-title":"Virol J"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3109\/10408361003633318","article-title":"Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections","volume":"47","author":"TT Lam","year":"2010","journal-title":"Crit Rev Clin Lab 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