{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T12:33:34Z","timestamp":1784637214628,"version":"3.55.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1006510","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T00:00:00Z","timestamp":1502323200000}}],"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2017,7,31]],"date-time":"2017-07-31T00:00:00Z","timestamp":1501459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"U.S. Department of Defense (US)","award":["W81XWH-07-2-0067"],"award-info":[{"award-number":["W81XWH-07-2-0067"]}]},{"name":"U.S. Department of Defense (US)","award":["W81XWH-11-0174"],"award-info":[{"award-number":["W81XWH-11-0174"]}]},{"name":"National Institute of Allergy and Infectious Diseases (US)","award":["Y1-AI-2642-17"],"award-info":[{"award-number":["Y1-AI-2642-17"]}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1006510","type":"journal-article","created":{"date-parts":[[2017,7,31]],"date-time":"2017-07-31T20:30:05Z","timestamp":1501533005000},"page":"e1006510","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":50,"title":["Rare HIV-1 transmitted\/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2746-9533","authenticated-orcid":true,"given":"Gustavo H.","family":"Kijak","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Sanders-Buell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnes-Laurence","family":"Chenine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3905-4877","authenticated-orcid":true,"given":"Michael A.","family":"Eller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilu","family":"Goonetilleke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rasmi","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8315-3146","authenticated-orcid":true,"given":"Sivan","family":"Leviyang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Harbolick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meera","family":"Bose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phuc","family":"Pham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Celina","family":"Oropeza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kultida","family":"Poltavee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne Marie","family":"O\u2019Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8963-0484","authenticated-orcid":true,"given":"Erik","family":"Billings","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5641-8612","authenticated-orcid":true,"given":"Melanie","family":"Merbah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret C.","family":"Costanzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna A.","family":"Warren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bonnie","family":"Slike","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina K.","family":"Peachman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4579-4062","authenticated-orcid":true,"given":"Will","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Cicala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Arthos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2043-1513","authenticated-orcid":true,"given":"Leigh A.","family":"Eller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert J.","family":"O\u2019Connell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Sinei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas","family":"Maganga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2293-1944","authenticated-orcid":true,"given":"Hannah","family":"Kibuuka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6935-1405","authenticated-orcid":true,"given":"Sorachai","family":"Nitayaphan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mangala","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary A.","family":"Marovich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelly J.","family":"Krebs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgane","family":"Rolland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2026-5757","authenticated-orcid":true,"given":"Bette T.","family":"Korber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George M.","family":"Shaw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5882-5548","authenticated-orcid":true,"given":"Nelson L.","family":"Michael","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3949-9649","authenticated-orcid":true,"given":"Merlin L.","family":"Robb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5946-4227","authenticated-orcid":true,"given":"Sodsai","family":"Tovanabutra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0461-6438","authenticated-orcid":true,"given":"Jerome H.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,7,31]]},"reference":[{"key":"ref1","unstructured":"(UNAIDS) JUNPoHA. The gap report. Geneva, Switzerland2014."},{"issue":"8","key":"ref2","doi-asserted-by":"crossref","first-page":"620","DOI":"10.7326\/0003-4819-138-8-200304150-00007","article-title":"Survival benefit of initiating antiretroviral therapy in HIV-infected persons in different CD4+ cell strata","volume":"138","author":"FJ Palella Jr.","year":"2003","journal-title":"Ann Intern Med"},{"issue":"4","key":"ref3","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1001\/jama.2014.17454","article-title":"Focusing to achieve a world without AIDS","volume":"313","author":"AS Fauci","year":"2015","journal-title":"JAMA"},{"issue":"11","key":"ref4","article-title":"HIV transmission","volume":"2","author":"GM Shaw","year":"2012","journal-title":"Cold Spring Harb Perspect Med"},{"issue":"22","key":"ref5","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1056\/NEJMoa1508952","article-title":"Prospective Study of Acute HIV-1 Infection in Adults in East Africa and Thailand","volume":"374","author":"ML Robb","year":"2016","journal-title":"N Engl J Med"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1146\/annurev-med-080709-124959","article-title":"Early events in sexual transmission of HIV and SIV and opportunities for interventions","volume":"62","author":"AT Haase","year":"2011","journal-title":"Annu Rev Med"},{"issue":"14","key":"ref7","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1056\/NEJM199104043241404","article-title":"High titers of cytopathic virus in plasma of patients with symptomatic primary HIV-1 infection","volume":"324","author":"SJ Clark","year":"1991","journal-title":"N Engl J Med"},{"issue":"14","key":"ref8","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1056\/NEJM199104043241405","article-title":"Transient high levels of viremia in patients with primary human immunodeficiency virus type 1 infection","volume":"324","author":"ES Daar","year":"1991","journal-title":"N Engl J Med"},{"issue":"6","key":"ref9","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1084\/jem.20040874","article-title":"CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract","volume":"200","author":"JM Brenchley","year":"2004","journal-title":"J Exp Med"},{"issue":"6","key":"ref10","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1084\/jem.20041196","article-title":"Primary HIV-1 infection is associated with preferential depletion of CD4+ T lymphocytes from effector sites in the gastrointestinal tract","volume":"200","author":"S Mehandru","year":"2004","journal-title":"J Exp Med"},{"issue":"8","key":"ref11","doi-asserted-by":"crossref","first-page":"3719","DOI":"10.1128\/JVI.01844-08","article-title":"Induction of a striking systemic cytokine cascade prior to peak viremia in acute human immunodeficiency virus type 1 infection, in contrast to more modest and delayed responses in acute hepatitis B and C virus infections","volume":"83","author":"AR Stacey","year":"2009","journal-title":"J Virol"},{"issue":"6","key":"ref12","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1084\/jem.20090365","article-title":"The first T cell response to transmitted\/founder virus contributes to the control of acute viremia in HIV-1 infection","volume":"206","author":"N Goonetilleke","year":"2009","journal-title":"J Exp Med"},{"issue":"7","key":"ref13","doi-asserted-by":"crossref","first-page":"4650","DOI":"10.1128\/JVI.68.7.4650-4655.1994","article-title":"Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome","volume":"68","author":"RA Koup","year":"1994","journal-title":"J Virol"},{"issue":"6929","key":"ref14","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature01470","article-title":"Antibody neutralization and escape by HIV-1","volume":"422","author":"X Wei","year":"2003","journal-title":"Nature"},{"issue":"6","key":"ref15","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1111\/j.1365-2796.2011.02457.x","article-title":"HIV reservoirs and the possibility of a cure for HIV infection","volume":"270","author":"S Palmer","year":"2011","journal-title":"J Intern Med"},{"issue":"9","key":"ref16","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1093\/infdis\/jiv219","article-title":"The Remarkable Stability of the Latent Reservoir for HIV-1 in Resting Memory CD4+ T Cells","volume":"212","author":"JM Siliciano","year":"2015","journal-title":"J Infect Dis"},{"issue":"7512","key":"ref17","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/nature13594","article-title":"Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys","volume":"512","author":"JB Whitney","year":"2014","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.ebiom.2016.07.024","article-title":"HIV DNA Set Point is Rapidly Established in Acute HIV Infection and Dramatically Reduced by Early ART","volume":"11","author":"J Ananworanich","year":"2016","journal-title":"EBioMedicine"},{"issue":"4","key":"ref19","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.coi.2006.05.001","article-title":"Immunopathogenesis of acute AIDS virus infection","volume":"18","author":"LJ Picker","year":"2006","journal-title":"Curr Opin Immunol"},{"issue":"12","key":"ref20","doi-asserted-by":"crossref","first-page":"946","DOI":"10.7326\/0003-4819-126-12-199706150-00003","article-title":"Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection","volume":"126","author":"JW Mellors","year":"1997","journal-title":"Ann Intern Med"},{"issue":"21","key":"ref21","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":"ref22","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":"1","key":"ref23","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":"6","key":"ref24","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":"2","key":"ref25","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.virol.2010.12.027","article-title":"Defining the human immunodeficiency virus type 1 transmission genetic bottleneck in a region with multiple circulating subtypes and recombinant forms","volume":"415","author":"A Nofemela","year":"2011","journal-title":"Virology"},{"issue":"6193","key":"ref26","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":"5","key":"ref27","doi-asserted-by":"crossref","first-page":"e1005619","DOI":"10.1371\/journal.ppat.1005619","article-title":"Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus","volume":"12","author":"DC Tully","year":"2016","journal-title":"PLoS Pathog."},{"issue":"15","key":"ref28","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":"1","key":"ref29","first-page":"380","article-title":"Vertical T cell immunodominance and epitope entropy determine HIV-1 escape","volume":"123","author":"MK Liu","year":"2013","journal-title":"J Clin Invest"},{"issue":"8","key":"ref30","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":"3","key":"ref31","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":"4","key":"ref32","first-page":"280","article-title":"Using nonhuman primates to model HIV transmission","volume":"8","author":"CM Fennessey","year":"2013","journal-title":"Curr Opin HIV AIDS"},{"issue":"12","key":"ref33","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"},{"issue":"3","key":"ref34","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/j.immuni.2015.08.012","article-title":"Magnitude and Kinetics of CD8+ T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point","volume":"43","author":"ZM Ndhlovu","year":"2015","journal-title":"Immunity"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.jviromet.2014.04.017","article-title":"Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform","volume":"205","author":"GH Kijak","year":"2014","journal-title":"J Virol Methods"},{"issue":"8","key":"ref36","doi-asserted-by":"crossref","first-page":"4005","DOI":"10.1128\/JVI.02785-15","article-title":"Expansion of Inefficient HIV-Specific CD8 T Cells during Acute Infection","volume":"90","author":"MA Eller","year":"2016","journal-title":"J Virol"},{"issue":"Suppl 2","key":"ref37","doi-asserted-by":"crossref","first-page":"S309","DOI":"10.1086\/655653","article-title":"Viral evolution and escape during acute HIV-1 infection","volume":"202","author":"CL Boutwell","year":"2010","journal-title":"J Infect Dis"},{"issue":"17","key":"ref38","doi-asserted-by":"crossref","first-page":"8548","DOI":"10.1128\/JVI.00580-08","article-title":"Central role of reverting mutations in HLA associations with human immunodeficiency virus set point","volume":"82","author":"PC Matthews","year":"2008","journal-title":"J Virol"},{"issue":"5","key":"ref39","doi-asserted-by":"crossref","first-page":"e1000414","DOI":"10.1371\/journal.ppat.1000414","article-title":"HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC","volume":"5","author":"N Wood","year":"2009","journal-title":"PLoS Pathog"},{"issue":"3","key":"ref40","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1016\/j.jmb.2004.01.046","article-title":"Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo","volume":"337","author":"RC Beale","year":"2004","journal-title":"J Mol Biol"},{"issue":"15","key":"ref41","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1016\/j.cub.2004.06.050","article-title":"APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo","volume":"14","author":"MT Liddament","year":"2004","journal-title":"Curr Biol"},{"issue":"3","key":"ref42","doi-asserted-by":"crossref","first-page":"e24","DOI":"10.1371\/journal.pcbi.0020024","article-title":"Estimating Costs and Benefits of CTL Escape Mutations in SIV\/HIV Infection","volume":"2","author":"VV Ganusov","year":"2006","journal-title":"PLoS Comput Biol"},{"issue":"9","key":"ref43","doi-asserted-by":"crossref","first-page":"5721","DOI":"10.1128\/JVI.79.9.5721-5731.2005","article-title":"Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost","volume":"79","author":"CS Fernandez","year":"2005","journal-title":"J Virol"},{"issue":"19","key":"ref44","doi-asserted-by":"crossref","first-page":"8035","DOI":"10.1073\/pnas.0608832104","article-title":"In vivo T lymphocyte dynamics in humans and the impact of human T-lymphotropic virus 1 infection","volume":"104","author":"B Asquith","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nri3787","article-title":"Type I interferons in infectious disease","volume":"15","author":"F McNab","year":"2015","journal-title":"Nat Rev Immunol"},{"key":"ref46","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":"12","key":"ref47","doi-asserted-by":"crossref","first-page":"e1004543","DOI":"10.1371\/journal.ppat.1004543","article-title":"Initiation of ART during early acute HIV infection preserves mucosal Th17 function and reverses HIV-related immune activation","volume":"10","author":"A Schuetz","year":"2014","journal-title":"PLoS Pathog"},{"issue":"3","key":"ref48","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/ni1566","article-title":"HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells","volume":"9","author":"J Arthos","year":"2008","journal-title":"Nat Immunol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s12977-014-0069-9","article-title":"Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection","volume":"11","author":"AJ Ritchie","year":"2014","journal-title":"Retrovirology"},{"issue":"14","key":"ref50","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":"10","key":"ref51","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1093\/infdis\/jit485","article-title":"Molecular mechanisms of HIV type 1 prophylaxis failure revealed by single-genome sequencing","volume":"208","author":"H Li","year":"2013","journal-title":"J Infect Dis"},{"issue":"7511","key":"ref52","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nature13554","article-title":"Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression","volume":"511","author":"NG Sandler","year":"2014","journal-title":"Nature"},{"issue":"5","key":"ref53","doi-asserted-by":"crossref","first-page":"e1002048","DOI":"10.1371\/journal.ppat.1002048","article-title":"Viral CTL escape mutants are generated in lymph nodes and subsequently become fixed in plasma and rectal mucosa during acute SIV infection of macaques","volume":"7","author":"TH Vanderford","year":"2011","journal-title":"PLoS Pathog"},{"issue":"18","key":"ref54","doi-asserted-by":"crossref","first-page":"10096","DOI":"10.1128\/JVI.78.18.10096-10103.2004","article-title":"Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection","volume":"78","author":"MP Davenport","year":"2004","journal-title":"J Virol"},{"issue":"4","key":"ref55","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1371\/journal.pbio.0040090","article-title":"Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo","volume":"4","author":"B Asquith","year":"2006","journal-title":"PLoS Biol"},{"issue":"19","key":"ref56","doi-asserted-by":"crossref","first-page":"9519","DOI":"10.1128\/JVI.00575-06","article-title":"Selection on the human immunodeficiency virus type 1 proteome following primary infection","volume":"80","author":"Y Liu","year":"2006","journal-title":"J Virol"},{"issue":"2","key":"ref57","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nm0297-205","article-title":"Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus","volume":"3","author":"P Borrow","year":"1997","journal-title":"Nat Med"},{"issue":"20","key":"ref58","doi-asserted-by":"crossref","first-page":"10303","DOI":"10.1128\/JVI.01876-15","article-title":"Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection","volume":"89","author":"JE Sunshine","year":"2015","journal-title":"J Virol"},{"issue":"3","key":"ref59","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.immuni.2012.11.021","article-title":"A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells","volume":"38","author":"K Ladell","year":"2013","journal-title":"Immunity"},{"issue":"3","key":"ref60","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/nm992","article-title":"HIV evolution: CTL escape mutation and reversion after transmission","volume":"10","author":"AJ Leslie","year":"2004","journal-title":"Nat Med"},{"issue":"10","key":"ref61","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1038\/nm.3932","article-title":"HIV-1 infections with multiple founders are associated with higher viral loads than infections with single founders","volume":"21","author":"H Janes","year":"2015","journal-title":"Nat Med"},{"issue":"11","key":"ref62","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1038\/nm.3963","article-title":"Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies","volume":"21","author":"JN Bhiman","year":"2015","journal-title":"Nat Med"},{"issue":"50","key":"ref63","doi-asserted-by":"crossref","first-page":"20166","DOI":"10.1073\/pnas.1110064108","article-title":"Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID","volume":"108","author":"CB Jabara","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref64","article-title":"On the duration of the period between exposure to HIV and detectable infection","author":"BP Konrad","year":"2017","journal-title":"Epidemics"},{"issue":"8","key":"ref65","doi-asserted-by":"crossref","first-page":"e1001053","DOI":"10.1371\/journal.ppat.1001053","article-title":"HIV-1 Populations in Semen Arise through Multiple Mechanisms","volume":"6","author":"JA Anderson","year":"2010","journal-title":"PLoS Pathog"},{"issue":"9","key":"ref66","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":"5","key":"ref67","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":"11","key":"ref68","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":"5","key":"ref69","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":"13","key":"ref70","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":"2","key":"ref71","doi-asserted-by":"crossref","first-page":"e1003973","DOI":"10.1371\/journal.pcbi.1003973","article-title":"Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial","volume":"11","author":"PT Edlefsen","year":"2015","journal-title":"PLoS Comput Biol"},{"issue":"10","key":"ref72","doi-asserted-by":"crossref","first-page":"e76502","DOI":"10.1371\/journal.pone.0076502","article-title":"Improved detection of rare HIV-1 variants using 454 pyrosequencing","volume":"8","author":"BB Larsen","year":"2013","journal-title":"PLoS One"},{"key":"ref73","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":"12","key":"ref74","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"M Kearse","year":"2012","journal-title":"Bioinformatics"},{"issue":"12","key":"ref75","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0","volume":"30","author":"K Tamura","year":"2013","journal-title":"Mol Biol Evol"},{"key":"ref76","article-title":"Human Retroviruses and AIDS","author":"B Korber","year":"1998"},{"issue":"1","key":"ref77","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1093\/bioinformatics\/btq614","article-title":"SAMStat: monitoring biases in next generation sequencing data","volume":"27","author":"T Lassmann","year":"2011","journal-title":"Bioinformatics"},{"issue":"10","key":"ref78","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1089\/aid.2013.0175","article-title":"Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data","volume":"29","author":"GH Kijak","year":"2013","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"2","key":"ref79","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/bib\/bbs012","article-title":"Using Tablet for visual exploration of second-generation sequencing data","volume":"14","author":"I Milne","year":"2013","journal-title":"Brief Bioinform"},{"issue":"7588","key":"ref80","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature16933","article-title":"Persistent HIV-1 replication maintains the tissue reservoir during therapy","volume":"530","author":"R Lorenzo-Redondo","year":"2016","journal-title":"Nature"},{"issue":"11","key":"ref81","doi-asserted-by":"crossref","first-page":"e76104","DOI":"10.1371\/journal.pone.0076104","article-title":"Impact of HIV-1 backbone on neutralization sensitivity: neutralization profiles of heterologous envelope glycoproteins expressed in native subtype C and CRF01_AE backbone","volume":"8","author":"AL Chenine","year":"2013","journal-title":"PLoS One"},{"issue":"4","key":"ref82","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1038\/mt.2008.6","article-title":"A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis","volume":"16","author":"K Weber","year":"2008","journal-title":"Mol Ther"},{"issue":"9","key":"ref83","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1089\/088922203769232601","article-title":"Specific antibody responses to vaccination with bivalent CM235\/SF2 gp120: detection of homologous and heterologous neutralizing antibody to subtype E (CRF01.AE) HIV type 1","volume":"19","author":"JH Kim","year":"2003","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"3","key":"ref84","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/infdis\/jis367","article-title":"Magnitude and breadth of the neutralizing antibody response in the RV144 and Vax003 HIV-1 vaccine efficacy trials","volume":"206","author":"DC Montefiori","year":"2012","journal-title":"J Infect Dis"},{"issue":"4","key":"ref85","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.4049\/jimmunol.133.4.1857","article-title":"Lymphocyte activation antigens. I. A monoclonal antibody, anti-Act I, defines a new late lymphocyte activation antigen","volume":"133","author":"AI Lazarovits","year":"1984","journal-title":"J Immunol"},{"issue":"5","key":"ref86","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1007\/s00251-014-0765-6","article-title":"HLA class I, KIR, and genome-wide SNP diversity in the RV144 Thai phase 3 HIV vaccine clinical trial","volume":"66","author":"HA Prentice","year":"2014","journal-title":"Immunogenetics"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1006620","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2017,9,14]],"date-time":"2017-09-14T00:00:00Z","timestamp":1505347200000}},{"DOI":"10.1371\/journal.ppat.1006510","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,8,10]],"date-time":"2017-08-10T00:00:00Z","timestamp":1502323200000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1006510","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,24]],"date-time":"2023-08-24T19:46:36Z","timestamp":1692906396000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1006510"}},"subtitle":[],"editor":[{"given":"Daniel C.","family":"Douek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,7,31]]},"references-count":86,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2017,7,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1006510","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.ppat.1006620","asserted-by":"object"}],"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1006510","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,31]]}}}