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Soft selective sweeps in evolutionary rescue. bioRxiv. 2016.","DOI":"10.1101\/052993"},{"issue":"14","key":"ref70","doi-asserted-by":"crossref","first-page":"8077","DOI":"10.1128\/JVI.01026-14","article-title":"Molecularly tagged simian immunodeficiency virus SIVmac239 synthetic swarm for tracking independent infection events","volume":"88","author":"GQ Del Prete","year":"2014","journal-title":"J Virol"},{"issue":"2","key":"ref71","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1128\/JVI.01691-07","article-title":"Removal of a single N-linked glycan in human immunodeficiency virus type 1 gp120 results in an enhanced ability to induce neutralizing antibody responses","volume":"82","author":"Y Li","year":"2008","journal-title":"J Virol"},{"issue":"4\u20135","key":"ref72","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1111\/j.1600-0684.2007.00243.x","article-title":"Immunogenicity and protective efficacy of Gag\/Pol\/Env vaccines derived from temporal isolates of SIVmne against cognate virus challenge","volume":"36","author":"P Polacino","year":"2007","journal-title":"J Med Primatol"},{"issue":"2","key":"ref73","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1089\/aid.1998.14.183","article-title":"Plasma SIV RNA viral load determination by real-time quantification of product generation in reverse transcriptase-polymerase chain reaction","volume":"14","author":"K Suryanarayana","year":"1998","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/1742-4690-6-65","article-title":"Pathogenic infection of Macaca nemestrina with a CCR5-tropic subtype-C simian-human immunodeficiency virus","volume":"6","author":"O Ho","year":"2009","journal-title":"Retrovirology"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"e84275","DOI":"10.1371\/journal.pone.0084275","article-title":"Persistence of viral reservoirs in multiple tissues after antiretroviral therapy suppression in a macaque RT-SHIV model","volume":"8","author":"C Kline","year":"2013","journal-title":"PloS one"},{"key":"ref76","first-page":"132","article-title":"2015 Update of the Drug Resistance Mutations in HIV-1","author":"AM Wensing","year":"2015","journal-title":"Topics in Antiviral Medicine"},{"issue":"5","key":"ref77","doi-asserted-by":"crossref","first-page":"2944","DOI":"10.1128\/AAC.04952-14","article-title":"Mass spectrometry imaging reveals heterogeneous efavirenz distribution within putative HIV reservoirs","volume":"59","author":"CG Thompson","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"ref78","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1093\/infdis\/jiw077","article-title":"A Translational Pharmacology Approach to Predicting Outcomes of Preexposure Prophylaxis Against HIV in Men and Women Using Tenofovir Disoproxil Fumarate With or Without Emtricitabine","volume":"214","author":"ML Cottrell","year":"2016","journal-title":"J Infect Dis"},{"key":"ref79","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":"Molecular biology and evolution"},{"key":"ref80","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":"Journal of molecular evolution"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"G Yu","year":"2017","journal-title":"Methods in Ecology and Evolution"},{"key":"ref82","article-title":"Elements of Evolutionary Genetics","author":"B Charlesworth","year":"2010"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1902","DOI":"10.1093\/molbev\/msh196","article-title":"A robust measure of HIV-1 population turnover within chronically infected individuals","volume":"21","author":"G Achaz","year":"2004","journal-title":"Molecular biology and evolution"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"e281","DOI":"10.7717\/peerj.281","article-title":"Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and\/or sexual reproduction","volume":"2","author":"ZN Kamvar","year":"2014","journal-title":"PeerJ"},{"issue":"5","key":"ref85","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/bti079","article-title":"HyPhy: hypothesis testing using phylogenies","volume":"21","author":"SLK Pond","year":"2005","journal-title":"Bioinformatics"},{"issue":"14","key":"ref86","doi-asserted-by":"crossref","first-page":"7142","DOI":"10.1128\/JVI.01955-10","article-title":"Different regions of HIV-1 subtype C env are associated with placental localization and in utero mother-to-child transmission","volume":"85","author":"SB Kumar","year":"2011","journal-title":"J Virol"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"9864","DOI":"10.1128\/JVI.00915-10","article-title":"Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication","volume":"84","author":"ME Abram","year":"2010","journal-title":"Journal of virology"}],"container-title":["PLOS 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