{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T13:25:47Z","timestamp":1790429147525,"version":"4.1.0"},"reference-count":115,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2016,5,10]],"date-time":"2016-05-10T00:00:00Z","timestamp":1462838400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["P01 AI074415"],"award-info":[{"award-number":["P01 AI074415"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001117","name":"amfAR, The Foundation for AIDS Research","doi-asserted-by":"publisher","award":["108683-55-RKMT"],"award-info":[{"award-number":["108683-55-RKMT"]}],"id":[{"id":"10.13039\/100001117","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000245","name":"Michael Smith Foundation for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["P01 AI074415"],"award-info":[{"award-number":["P01 AI074415"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jane Brock-Wilson Fund"},{"DOI":"10.13039\/100007301","name":"Harvard University Center for AIDS Research","doi-asserted-by":"publisher","award":["2P30 AI060354-11"],"award-info":[{"award-number":["2P30 AI060354-11"]}],"id":[{"id":"10.13039\/100007301","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1005619","type":"journal-article","created":{"date-parts":[[2016,5,10]],"date-time":"2016-05-10T13:26:30Z","timestamp":1462886790000},"page":"e1005619","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":99,"title":["Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus"],"prefix":"10.1371","volume":"12","author":[{"given":"Damien C.","family":"Tully","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin B.","family":"Ogilvie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca E.","family":"Batorsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Bean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen A.","family":"Power","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Musie","family":"Ghebremichael","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hunter E.","family":"Bedard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrianne D.","family":"Gladden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron M.","family":"Seese","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly A.","family":"Amero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly","family":"Lane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham","family":"McGrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzane B.","family":"Bazner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jake","family":"Tinsley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niall J.","family":"Lennon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew R.","family":"Henn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zabrina L.","family":"Brumme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip J.","family":"Norris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric S.","family":"Rosenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth H.","family":"Mayer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heiko","family":"Jessen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce D.","family":"Walker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Altfeld","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M.","family":"Carlson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd M.","family":"Allen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,5,10]]},"reference":[{"key":"ref1","unstructured":"UNAIDS. 2013."},{"issue":"6","key":"ref2","doi-asserted-by":"crossref","first-page":"3345","DOI":"10.1128\/JVI.67.6.3345-3356.1993","article-title":"Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection","volume":"67","author":"LQ Zhang","year":"1993","journal-title":"J Virol"},{"issue":"5048","key":"ref3","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1126\/science.1546316","article-title":"Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants","volume":"255","author":"SM Wolinsky","year":"1992","journal-title":"Science"},{"issue":"5125","key":"ref4","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1126\/science.8356453","article-title":"Genotypic and phenotypic characterization of HIV-1 patients with primary infection","volume":"261","author":"T Zhu","year":"1993","journal-title":"Science"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0042-6822(92)90685-I","article-title":"HIV-1 genomic RNA diversification following sexual and parenteral virus transmission","volume":"189","author":"TF Wolfs","year":"1992","journal-title":"Virology"},{"issue":"21","key":"ref6","doi-asserted-by":"crossref","first-page":"10247","DOI":"10.1073\/pnas.89.21.10247","article-title":"Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease","volume":"89","author":"T McNearney","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ref7","doi-asserted-by":"crossref","first-page":"e1000274","DOI":"10.1371\/journal.ppat.1000274","article-title":"Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1","volume":"5","author":"RE Haaland","year":"2009","journal-title":"PLoS Pathog"},{"issue":"15","key":"ref8","doi-asserted-by":"crossref","first-page":"5640","DOI":"10.1073\/pnas.0308425101","article-title":"Roles of substrate availability and infection of resting and activated CD4+ T cells in transmission and acute simian immunodeficiency virus infection","volume":"101","author":"ZQ Zhang","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1093\/infdis\/jis465","article-title":"Innate immune activation enhances hiv acquisition in women, diminishing the effectiveness of tenofovir microbicide gel","volume":"206","author":"V Naranbhai","year":"2012","journal-title":"J Infect Dis"},{"issue":"13","key":"ref10","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1097\/00002030-199813000-00019","article-title":"Bacterial vaginosis and disturbances of vaginal flora: association with increased acquisition of HIV","volume":"12","author":"TE Taha","year":"1998","journal-title":"AIDS"},{"issue":"1","key":"ref11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/nrmicro794","article-title":"The role of sexually transmitted diseases in HIV transmission","volume":"2","author":"SR Galvin","year":"2004","journal-title":"Nat Rev Microbiol"},{"issue":"6193","key":"ref12","doi-asserted-by":"crossref","first-page":"1254031","DOI":"10.1126\/science.1254031","article-title":"HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck","volume":"345","author":"JM Carlson","year":"2014","journal-title":"Science"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.jtbi.2009.07.038","article-title":"Modeling sequence evolution in acute HIV-1 infection","volume":"261","author":"HY Lee","year":"2009","journal-title":"J Theor Biol"},{"issue":"21","key":"ref14","doi-asserted-by":"crossref","first-page":"7552","DOI":"10.1073\/pnas.0802203105","article-title":"Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection","volume":"105","author":"BF Keele","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"ref15","doi-asserted-by":"crossref","first-page":"3556","DOI":"10.1128\/JVI.02132-08","article-title":"Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants","volume":"83","author":"MR Abrahams","year":"2009","journal-title":"J Virol"},{"issue":"6","key":"ref16","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1084\/jem.20090378","article-title":"Genetic identity, biological phenotype, and evolutionary pathways of transmitted\/founder viruses in acute and early HIV-1 infection","volume":"206","author":"JF Salazar-Gonzalez","year":"2009","journal-title":"J Exp Med"},{"issue":"8","key":"ref17","doi-asserted-by":"crossref","first-page":"3952","DOI":"10.1128\/JVI.02660-07","article-title":"Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing","volume":"82","author":"JF Salazar-Gonzalez","year":"2008","journal-title":"J Virol"},{"issue":"8","key":"ref18","doi-asserted-by":"crossref","first-page":"e12303","DOI":"10.1371\/journal.pone.0012303","article-title":"Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing","volume":"5","author":"W Fischer","year":"2010","journal-title":"PLoS One"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"e1000890","DOI":"10.1371\/journal.ppat.1000890","article-title":"High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men","volume":"6","author":"H Li","year":"2010","journal-title":"PLoS Pathog"},{"issue":"10","key":"ref20","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1097\/QAD.0000000000000298","article-title":"Estimating per-act HIV transmission risk: a systematic review","volume":"28","author":"P Patel","year":"2014","journal-title":"AIDS"},{"issue":"5666","key":"ref21","doi-asserted-by":"crossref","first-page":"2019","DOI":"10.1126\/science.1093137","article-title":"Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission","volume":"303","author":"CA Derdeyn","year":"2004","journal-title":"Science"},{"issue":"8","key":"ref22","doi-asserted-by":"crossref","first-page":"4185","DOI":"10.1128\/JVI.02297-12","article-title":"Antigenicity and immunogenicity of transmitted\/founder, consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1","volume":"87","author":"HX Liao","year":"2013","journal-title":"J Virol"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"2401","DOI":"10.1128\/JVI.02964-12","article-title":"Transmitted\/founder and chronic HIV-1 envelope proteins are distinguished by differential utilization of CCR5","volume":"87","author":"ZF Parker","year":"2013","journal-title":"J Virol"},{"issue":"13","key":"ref24","doi-asserted-by":"crossref","first-page":"7218","DOI":"10.1128\/JVI.03577-12","article-title":"Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design","volume":"87","author":"LH Ping","year":"2013","journal-title":"J Virol"},{"issue":"17","key":"ref25","doi-asserted-by":"crossref","first-page":"8514","DOI":"10.1128\/JVI.00736-11","article-title":"Phenotypic and immunologic comparison of clade B transmitted\/founder and chronic HIV-1 envelope glycoproteins","volume":"85","author":"CB Wilen","year":"2011","journal-title":"J Virol"},{"issue":"5","key":"ref26","doi-asserted-by":"crossref","first-page":"e1002686","DOI":"10.1371\/journal.ppat.1002686","article-title":"Transmitted\/founder and chronic subtype C HIV-1 use CD4 and CCR5 receptors with equal efficiency and are not inhibited by blocking the integrin alpha4beta7","volume":"8","author":"NF Parrish","year":"2012","journal-title":"PLoS Pathog"},{"issue":"17","key":"ref27","doi-asserted-by":"crossref","first-page":"6626","DOI":"10.1073\/pnas.1304288110","article-title":"Phenotypic properties of transmitted founder HIV-1","volume":"110","author":"NF Parrish","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ref28","doi-asserted-by":"crossref","first-page":"e1001301","DOI":"10.1371\/journal.ppat.1001301","article-title":"The genotype of early-transmitting HIV gp120s promotes alpha (4) beta(7)-reactivity, revealing alpha (4) beta(7) +\/CD4+ T cells as key targets in mucosal transmission","volume":"7","author":"F Nawaz","year":"2011","journal-title":"PLoS Pathog"},{"issue":"4","key":"ref29","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1128\/JVI.80.4.1637-1644.2006","article-title":"Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host","volume":"80","author":"JT Herbeck","year":"2006","journal-title":"J Virol"},{"issue":"9","key":"ref30","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1093\/infdis\/jis503","article-title":"Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions","volume":"206","author":"AD Redd","year":"2012","journal-title":"J Infect Dis"},{"issue":"10","key":"ref31","doi-asserted-by":"crossref","first-page":"6523","DOI":"10.1128\/JVI.79.10.6523-6527.2005","article-title":"Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B","volume":"79","author":"SD Frost","year":"2005","journal-title":"J Virol"},{"issue":"10","key":"ref32","doi-asserted-by":"crossref","first-page":"6528","DOI":"10.1128\/JVI.79.10.6528-6531.2005","article-title":"Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1\u2013V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels","volume":"79","author":"B Chohan","year":"2005","journal-title":"J Virol"},{"issue":"2","key":"ref33","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.virol.2008.01.029","article-title":"Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses","volume":"374","author":"Y Liu","year":"2008","journal-title":"Virology"},{"issue":"9","key":"ref34","doi-asserted-by":"crossref","first-page":"e1002209","DOI":"10.1371\/journal.ppat.1002209","article-title":"Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections","volume":"7","author":"S Gnanakaran","year":"2011","journal-title":"PLoS Pathog"},{"issue":"8","key":"ref35","doi-asserted-by":"crossref","first-page":"e23673","DOI":"10.1371\/journal.pone.0023673","article-title":"A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity","volume":"6","author":"M Asmal","year":"2011","journal-title":"PLoS One"},{"issue":"5","key":"ref36","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1128\/JVI.06157-11","article-title":"Generation of transmitted\/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages","volume":"86","author":"C Ochsenbauer","year":"2011","journal-title":"J Virol"},{"issue":"4","key":"ref37","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/nrmicro1387","article-title":"Selective transmission of CCR5-utilizing HIV-1: the 'gatekeeper' problem resolved?","volume":"4","author":"L Margolis","year":"2006","journal-title":"Nat Rev Microbiol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/1742-4690-10-146","article-title":"Relative resistance of HIV-1 founder viruses to control by interferon-alpha","volume":"10","author":"AE Fenton-May","year":"2013","journal-title":"Retrovirology"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/s12977-014-0106-8","article-title":"Characterization of HIV-1 envelopes in acutely and chronically infected injection drug users","volume":"11","author":"B Etemad","year":"2014","journal-title":"Retrovirology"},{"issue":"9","key":"ref40","doi-asserted-by":"crossref","first-page":"e1005154","DOI":"10.1371\/journal.ppat.1005154","article-title":"Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-alpha Resistance","volume":"11","author":"MJ Deymier","year":"2015","journal-title":"PLoS Pathog"},{"issue":"46","key":"ref41","doi-asserted-by":"crossref","first-page":"E1156","DOI":"10.1073\/pnas.1103764108","article-title":"Role of donor genital tract HIV-1 diversity in the transmission bottleneck","volume":"108","author":"DI Boeras","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/1742-4690-10-162","article-title":"HIV-1 envelope replication and alpha4beta7 utilization among newly infected subjects and their corresponding heterosexual partners","volume":"10","author":"V Pena-Cruz","year":"2013","journal-title":"Retrovirology"},{"issue":"4","key":"ref43","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1086\/596557","article-title":"Selection of HIV variants with signature genotypic characteristics during heterosexual transmission","volume":"199","author":"M Sagar","year":"2009","journal-title":"J Infect Dis"},{"issue":"15","key":"ref44","doi-asserted-by":"crossref","first-page":"7523","DOI":"10.1128\/JVI.02697-10","article-title":"Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes","volume":"85","author":"JT Herbeck","year":"2011","journal-title":"J Virol"},{"issue":"16","key":"ref45","doi-asserted-by":"crossref","first-page":"8208","DOI":"10.1128\/JVI.00296-09","article-title":"Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization","volume":"83","author":"J Isaacman-Beck","year":"2009","journal-title":"J Virol"},{"issue":"8","key":"ref46","doi-asserted-by":"crossref","first-page":"4100","DOI":"10.1128\/JVI.02068-09","article-title":"Donor and recipient envs from heterosexual human immunodeficiency virus subtype C transmission pairs require high receptor levels for entry","volume":"84","author":"M Alexander","year":"2010","journal-title":"J Virol"},{"issue":"11","key":"ref47","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1086\/652702","article-title":"A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia","volume":"201","author":"AE Masharsky","year":"2010","journal-title":"J Infect Dis"},{"issue":"7","key":"ref48","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1086\/529206","article-title":"HIV-1 variation before seroconversion in men who have sex with men: analysis of acute\/early HIV infection in the multicenter AIDS cohort study","volume":"197","author":"GS Gottlieb","year":"2008","journal-title":"J Infect Dis"},{"issue":"12","key":"ref49","doi-asserted-by":"crossref","first-page":"6241","DOI":"10.1128\/JVI.00077-10","article-title":"Wide variation in the multiplicity of HIV-1 infection among injection drug users","volume":"84","author":"KJ Bar","year":"2010","journal-title":"J Virol"},{"key":"ref50","unstructured":"Dukhovlinova E, Masharsky A, Verevochkin S, Toussova O, Shevchenko A, Montefiori D, et al. AHI Detection Among People Who Inject Drugs in Russia Reveals the HIV-1 Transmission Bottleneck. Conference On Retroviruses And Opportunistic Infections (CROI 2014): International Antiviral Society\u2014USA; 2014. p. 299."},{"issue":"3","key":"ref51","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1093\/molbev\/msu400","article-title":"RELAX: detecting relaxed selection in a phylogenetic framework","volume":"32","author":"JO Wertheim","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"5608","key":"ref52","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/267275a0","article-title":"Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution","volume":"267","author":"M Kimura","year":"1977","journal-title":"Nature"},{"issue":"12","key":"ref53","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/S0169-5347(00)01994-7","article-title":"Statistical methods for detecting molecular adaptation","volume":"15","author":"Z Yang","year":"2000","journal-title":"Trends Ecol Evol"},{"issue":"11","key":"ref54","doi-asserted-by":"crossref","first-page":"e1000225","DOI":"10.1371\/journal.pcbi.1000225","article-title":"Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag","volume":"4","author":"JM Carlson","year":"2008","journal-title":"PLoS Comput Biol"},{"issue":"5818","key":"ref55","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1126\/science.1131528","article-title":"Founder effects in the assessment of HIV polymorphisms and HLA allele associations","volume":"315","author":"T Bhattacharya","year":"2007","journal-title":"Science"},{"issue":"16","key":"ref56","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"JD Storey","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7028","key":"ref57","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03327","article-title":"Structure of an unliganded simian immunodeficiency virus gp120 core","volume":"433","author":"B Chen","year":"2005","journal-title":"Nature"},{"issue":"Pt 5","key":"ref58","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1099\/vir.0.017319-0","article-title":"Emergence of monoclonal antibody b12-resistant human immunodeficiency virus type 1 variants during natural infection in the absence of humoral or cellular immune pressure","volume":"91","author":"EM Bunnik","year":"2010","journal-title":"J Gen Virol"},{"issue":"47","key":"ref59","doi-asserted-by":"crossref","first-page":"36456","DOI":"10.1074\/jbc.M110.156588","article-title":"Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution","volume":"285","author":"I Bontjer","year":"2010","journal-title":"J Biol Chem"},{"issue":"41","key":"ref60","doi-asserted-by":"crossref","first-page":"15160","DOI":"10.1073\/pnas.0605513103","article-title":"The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia","volume":"103","author":"RL Dunfee","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1742-4690-9-36","article-title":"MiniCD4 protein resistance mutations affect binding to the HIV-1 gp120 CD4 binding site and decrease entry efficiency","volume":"9","author":"K Grupping","year":"2012","journal-title":"Retrovirology"},{"issue":"6","key":"ref62","doi-asserted-by":"crossref","first-page":"2740","DOI":"10.1128\/JVI.02180-09","article-title":"Evolution of the HIV-1 env gene in the Rag2-\/- gammaC-\/- humanized mouse model","volume":"84","author":"WL Ince","year":"2010","journal-title":"J Virol"},{"issue":"7","key":"ref63","doi-asserted-by":"crossref","first-page":"3742","DOI":"10.1128\/JVI.78.7.3742-3752.2004","article-title":"Localized changes in the gp120 envelope glycoprotein confer resistance to human immunodeficiency virus entry inhibitors BMS-806 and #155","volume":"78","author":"N Madani","year":"2004","journal-title":"J Virol"},{"issue":"9","key":"ref64","doi-asserted-by":"crossref","first-page":"6869","DOI":"10.1128\/JVI.71.9.6869-6874.1997","article-title":"Human immunodeficiency virus type 1 mutants that escape neutralization by human monoclonal antibody IgG1b12. off","volume":"71","author":"H Mo","year":"1997","journal-title":"J Virol"},{"issue":"10","key":"ref65","doi-asserted-by":"crossref","first-page":"6179","DOI":"10.1128\/JVI.67.10.6179-6191.1993","article-title":"Strain specificity and binding affinity requirements of neutralizing monoclonal antibodies to the C4 domain of gp120 from human immunodeficiency virus type 1","volume":"67","author":"GR Nakamura","year":"1993","journal-title":"J Virol"},{"issue":"1","key":"ref66","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.virol.2003.12.012","article-title":"The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4","volume":"321","author":"P Pugach","year":"2004","journal-title":"Virology"},{"issue":"8","key":"ref67","doi-asserted-by":"crossref","first-page":"3757","DOI":"10.1128\/JVI.01544-06","article-title":"Impact of V2 mutations on escape from a potent neutralizing anti-V3 monoclonal antibody during in vitro selection of a primary human immunodeficiency virus type 1 isolate","volume":"81","author":"J Shibata","year":"2007","journal-title":"J Virol"},{"issue":"2","key":"ref68","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.virol.2010.12.010","article-title":"CD4-binding site alterations in CCR5-using HIV-1 envelopes influencing gp120-CD4 interactions and fusogenicity","volume":"410","author":"J Sterjovski","year":"2011","journal-title":"Virology"},{"issue":"1","key":"ref69","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1128\/JVI.69.1.39-48.1995","article-title":"Adaptation to persistent growth in the H9 cell line renders a primary isolate of human immunodeficiency virus type 1 sensitive to neutralization by vaccine sera","volume":"69","author":"T Wrin","year":"1995","journal-title":"J Virol"},{"issue":"Suppl 9","key":"ref70","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-14-S9-S2","article-title":"Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows","volume":"14","author":"P Skums","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"ref71","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gku537","article-title":"Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations","volume":"42","author":"FD Giallonardo","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ref72","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1089\/cmb.2009.0164","article-title":"Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction","volume":"17","author":"O Zagordi","year":"2010","journal-title":"J Comput Biol"},{"issue":"21","key":"ref73","doi-asserted-by":"crossref","first-page":"7400","DOI":"10.1093\/nar\/gkq655","article-title":"Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies","volume":"38","author":"O Zagordi","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ref74","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bioinformatics\/btr627","article-title":"QuRe: software for viral quasispecies reconstruction from next-generation sequencing data","volume":"28","author":"MC Prosperi","year":"2011","journal-title":"Bioinformatics"},{"issue":"12","key":"ref75","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1089\/aid.2010.0042","article-title":"Comparison of methods to detect HIV dual infection","volume":"26","author":"M Pacold","year":"2010","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"3","key":"ref76","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bib\/bbs081","article-title":"Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes","volume":"15","author":"M Schirmer","year":"2012","journal-title":"Brief Bioinform"},{"issue":"3","key":"ref77","doi-asserted-by":"crossref","first-page":"e1002529","DOI":"10.1371\/journal.ppat.1002529","article-title":"Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection","volume":"8","author":"MR Henn","year":"2012","journal-title":"PLoS Pathog"},{"issue":"3","key":"ref78","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/nm.2316","article-title":"Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial","volume":"17","author":"M Rolland","year":"2011","journal-title":"Nat Med"},{"issue":"7","key":"ref79","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1093\/infdis\/jit633","article-title":"Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States","volume":"209","author":"GA Wagner","year":"2013","journal-title":"J Infect Dis"},{"issue":"12","key":"ref80","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1093\/cid\/cir725","article-title":"Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection","volume":"53","author":"P Rieder","year":"2011","journal-title":"Clin Infect Dis"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1186\/1471-2105-11-532","article-title":"Estimating time since infection in early homogeneous HIV-1 samples using a poisson model","volume":"11","author":"EE Giorgi","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"ref82","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro3471","article-title":"Bottlenecks in HIV-1 transmission: insights from the study of founder viruses","volume":"13","author":"SB Joseph","year":"2015","journal-title":"Nat Rev Microbiol"},{"issue":"12","key":"ref83","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1089\/aid.2011.0090","article-title":"SIVmac251 is inefficiently transmitted to rhesus macaques by penile inoculation with a single SIVenv variant found in ramp-up phase plasma","volume":"27","author":"ZM Ma","year":"2011","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"10","key":"ref84","doi-asserted-by":"crossref","first-page":"e76367","DOI":"10.1371\/journal.pone.0076367","article-title":"Viral RNA levels and env variants in semen and tissues of mature male rhesus macaques infected with SIV by penile inoculation","volume":"8","author":"F Fieni","year":"2013","journal-title":"PLoS One"},{"issue":"5","key":"ref85","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1084\/jem.20082831","article-title":"Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1","volume":"206","author":"BF Keele","year":"2009","journal-title":"J Exp Med"},{"issue":"3","key":"ref86","doi-asserted-by":"crossref","first-page":"e1004729","DOI":"10.1371\/journal.ppat.1004729","article-title":"Visualization of HIV-1 interactions with penile and foreskin epithelia: clues for female-to-male HIV transmission","volume":"11","author":"MH Dinh","year":"2015","journal-title":"PLoS Pathog"},{"issue":"18","key":"ref87","doi-asserted-by":"crossref","first-page":"8390","DOI":"10.1128\/JVI.75.18.8390-8399.2001","article-title":"A preponderance of CCR5(+) CXCR4(+) mononuclear cells enhances gastrointestinal mucosal susceptibility to human immunodeficiency virus type 1 infection","volume":"75","author":"MA Poles","year":"2001","journal-title":"J Virol"},{"issue":"3","key":"ref88","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1097\/QAI.0b013e3182898392","article-title":"Comprehensive assessment of HIV target cells in the distal human gut suggests increasing HIV susceptibility toward the anus","volume":"63","author":"MJ McElrath","year":"2013","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"5","key":"ref89","doi-asserted-by":"crossref","first-page":"e19493","DOI":"10.1371\/journal.pone.0019493","article-title":"Rapid dissemination of SIV follows multisite entry after rectal inoculation","volume":"6","author":"P Ribeiro Dos Santos","year":"2011","journal-title":"PLoS One"},{"issue":"Pt 5","key":"ref90","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1099\/vir.0.81307-0","article-title":"Rapid dissemination of a pathogenic simian\/human immunodeficiency virus to systemic organs and active replication in lymphoid tissues following intrarectal infection","volume":"87","author":"A Miyake","year":"2006","journal-title":"J Gen Virol"},{"issue":"29","key":"ref91","doi-asserted-by":"crossref","first-page":"27284","DOI":"10.1074\/jbc.M414411200","article-title":"Alanine scanning mutants of the HIV gp41 loop","volume":"280","author":"A Jacobs","year":"2005","journal-title":"J Biol Chem"},{"issue":"1","key":"ref92","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/JVI.02053-12","article-title":"The tale of the long tail: the cytoplasmic domain of HIV-1 gp41","volume":"87","author":"TS Postler","year":"2013","journal-title":"J Virol"},{"issue":"1","key":"ref93","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1002\/bip.360290122","article-title":"The most highly amphiphilic alpha-helices include two amino acid segments in human immunodeficiency virus glycoprotein 41","volume":"29","author":"D Eisenberg","year":"1990","journal-title":"Biopolymers"},{"issue":"1","key":"ref94","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1089\/aid.1989.5.7","article-title":"Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein","volume":"5","author":"RM Venable","year":"1989","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"17","key":"ref95","doi-asserted-by":"crossref","first-page":"5157","DOI":"10.1021\/bi962935r","article-title":"A leucine zipper-like sequence from the cytoplasmic tail of the HIV-1 envelope glycoprotein binds and perturbs lipid bilayers","volume":"36","author":"Y Kliger","year":"1997","journal-title":"Biochemistry"},{"issue":"6","key":"ref96","doi-asserted-by":"crossref","first-page":"3634","DOI":"10.1128\/JVI.77.6.3634-3646.2003","article-title":"Rational site-directed mutations of the LLP-1 and LLP-2 lentivirus lytic peptide domains in the intracytoplasmic tail of human immunodeficiency virus type 1 gp41 indicate common functions in cell-cell fusion but distinct roles in virion envelope incorporation","volume":"77","author":"V Kalia","year":"2003","journal-title":"J Virol"},{"issue":"24","key":"ref97","doi-asserted-by":"crossref","first-page":"11717","DOI":"10.1128\/JVI.74.24.11717-11723.2000","article-title":"Mutational analysis of conserved domains within the cytoplasmic tail of gp41 from human immunodeficiency virus type 1: effects on glycoprotein incorporation and infectivity","volume":"74","author":"SC Piller","year":"2000","journal-title":"J Virol"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1742-4690-4-89","article-title":"Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS","volume":"4","author":"J Sterjovski","year":"2007","journal-title":"Retrovirology"},{"issue":"12","key":"ref99","doi-asserted-by":"crossref","first-page":"7493","DOI":"10.1128\/JVI.67.12.7493-7500.1993","article-title":"Immune escape by human immunodeficiency virus type 1 from neutralizing antibodies: evidence for multiple pathways","volume":"67","author":"BA Watkins","year":"1993","journal-title":"J Virol"},{"issue":"7541","key":"ref100","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nature14264","article-title":"AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges","volume":"519","author":"MR Gardner","year":"2015","journal-title":"Nature"},{"issue":"27","key":"ref101","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1056\/NEJMoa1011205","article-title":"Preexposure chemoprophylaxis for HIV prevention in men who have sex with men","volume":"363","author":"RM Grant","year":"2010","journal-title":"N Engl J Med"},{"issue":"1","key":"ref102","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1097\/QAI.0000000000000367","article-title":"HIV disease progression in seroconvertors from the CAPRISA 004 tenofovir gel pre-exposure prophylaxis trial","volume":"68","author":"NJ Garrett","year":"2015","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"2","key":"ref103","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1097\/QAD.0b013e32834dcd26","article-title":"Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men","volume":"26","author":"ME Pacold","year":"2011","journal-title":"AIDS"},{"issue":"23","key":"ref104","doi-asserted-by":"crossref","first-page":"12921","DOI":"10.1128\/JVI.77.23.12921-12926.2003","article-title":"Infection with multiple human immunodeficiency virus type 1 variants is associated with faster disease progression","volume":"77","author":"M Sagar","year":"2003","journal-title":"J Virol"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1742-4690-11-22","article-title":"The number and genetic relatedness of transmitted\/founder virus impact clinical outcome in vaginal R5 SHIVSF162P3N infection","volume":"11","author":"L Tsai","year":"2014","journal-title":"Retrovirology"},{"issue":"9409","key":"ref106","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0140-6736(04)15596-7","article-title":"Dual HIV-1 infection associated with rapid disease progression","volume":"363","author":"GS Gottlieb","year":"2004","journal-title":"Lancet"},{"issue":"4","key":"ref107","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/cid\/cir849","article-title":"HIV-1 dual infection is associated with faster CD4+ T-cell decline in a cohort of men with primary HIV infection","volume":"54","author":"M Cornelissen","year":"2012","journal-title":"Clin Infect Dis"},{"issue":"27","key":"ref108","doi-asserted-by":"crossref","first-page":"11181","DOI":"10.1073\/pnas.1103012108","article-title":"Limited or no protection by weakly or nonneutralizing antibodies against vaginal SHIV challenge of macaques compared with a strongly neutralizing antibody","volume":"108","author":"DR Burton","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"ref109","doi-asserted-by":"crossref","first-page":"e1005042","DOI":"10.1371\/journal.ppat.1005042","article-title":"Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques","volume":"11","author":"S Santra","year":"2015","journal-title":"PLoS Pathog"},{"issue":"3","key":"ref110","doi-asserted-by":"crossref","first-page":"e1002417","DOI":"10.1371\/journal.pcbi.1002417","article-title":"Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data","volume":"8","author":"AR Macalalad","year":"2012","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"ref111","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","article-title":"ART: a next-generation sequencing read simulator","volume":"28","author":"W Huang","year":"2012","journal-title":"Bioinformatics"},{"issue":"1","key":"ref112","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1128\/JCM.43.1.406-413.2005","article-title":"Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis","volume":"43","author":"S Palmer","year":"2005","journal-title":"J Clin Microbiol"},{"issue":"13","key":"ref113","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1097\/00002030-200309050-00005","article-title":"Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection","volume":"17","author":"EW Fiebig","year":"2003","journal-title":"AIDS"},{"issue":"3","key":"ref114","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"},{"issue":"9","key":"ref115","doi-asserted-by":"crossref","first-page":"5230","DOI":"10.1128\/JVI.06728-11","article-title":"Widespread impact of HLA restriction on immune control and escape pathways of HIV-1","volume":"86","author":"JM Carlson","year":"2012","journal-title":"J Virol"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1005619","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,19]],"date-time":"2020-09-19T13:19:08Z","timestamp":1600521548000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1005619"}},"subtitle":[],"editor":[{"given":"Ronald","family":"Swanstrom","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,5,10]]},"references-count":115,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2016,5,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1005619","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.726345108.793530998","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,5,10]]}}}