{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T19:19:36Z","timestamp":1789759176955,"version":"4.0.1"},"reference-count":72,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2016,7,19]],"date-time":"2016-07-19T00:00:00Z","timestamp":1468886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["38619"],"award-info":[{"award-number":["38619"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["1032144"],"award-info":[{"award-number":["1032144"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI51794"],"award-info":[{"award-number":["AI51794"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["67385"],"award-info":[{"award-number":["67385"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000061","name":"Fogarty International Center","doi-asserted-by":"publisher","award":["D43TW00231"],"award-info":[{"award-number":["D43TW00231"]}],"id":[{"id":"10.13039\/100000061","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.1005742","type":"journal-article","created":{"date-parts":[[2016,7,19]],"date-time":"2016-07-19T17:43:32Z","timestamp":1468950212000},"page":"e1005742","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":108,"title":["Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization"],"prefix":"10.1371","volume":"12","author":[{"given":"Cecilia","family":"Rademeyer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bette","family":"Korber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael S.","family":"Seaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena E.","family":"Giorgi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruwayhida","family":"Thebus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Robles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J.","family":"Sheward","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kshitij","family":"Wagh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2458-0519","authenticated-orcid":true,"given":"Jetta","family":"Garrity","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brittany R.","family":"Carey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongmei","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelli M.","family":"Greene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haili","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8888-8048","authenticated-orcid":true,"given":"Gama P.","family":"Bandawe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinny C.","family":"Marais","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thabo E.","family":"Diphoko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Hraber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"Tumba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Penny L.","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glenda E.","family":"Gray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Kublin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Juliana","family":"McElrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marion","family":"Vermeulen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keren","family":"Middelkoop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda-Gail","family":"Bekker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hoelscher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonard","family":"Maboko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Makhema","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Merlin L.","family":"Robb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salim","family":"Abdool Karim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quarraisha","family":"Abdool Karim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerome H.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatrice H.","family":"Hahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald","family":"Swanstrom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynn","family":"Morris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Montefiori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn","family":"Williamson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,7,19]]},"reference":[{"key":"ref1","first-page":"1","article-title":"Safety, pharmacokinetics and neutralization of the broadly neutralizing HIV-1 human monoclonal antibody VRC01 in healthy adults","author":"JE Ledgerwood","year":"2015","journal-title":"Clin Exp Immunol"},{"key":"ref2","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":"C a Derdeyn","year":"2004","journal-title":"Science"},{"key":"ref3","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"},{"key":"ref4","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":"M-R Abrahams","year":"2009","journal-title":"J Virol"},{"key":"ref5","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"},{"key":"ref6","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":"L-H Ping","year":"2013","journal-title":"J Virol"},{"key":"ref7","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"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"243ra88","DOI":"10.1126\/scitranslmed.3008992","article-title":"Neutralizing antibodies to HIV-1 envelope protect more effectively in vivo than those to the CD4 receptor","volume":"6","author":"A Pegu","year":"2014","journal-title":"Sci Transl Med"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"12669","DOI":"10.1128\/JVI.02213-14","article-title":"Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo","volume":"88","author":"RS Rudicell","year":"2014","journal-title":"J Virol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1056\/NEJMoa1113425","article-title":"Immune-correlates analysis of an HIV-1 vaccine efficacy trial","volume":"366","author":"BF Haynes","year":"2012","journal-title":"N Engl J Med"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.ebiom.2014.10.022","article-title":"Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses","volume":"1","author":"S Zolla-Pazner","year":"2014","journal-title":"EBioMedicine. Elsevier B.V"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e75665","DOI":"10.1371\/journal.pone.0075665","article-title":"Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial","volume":"8","author":"R Gottardo","year":"2013","journal-title":"PLoS One"},{"key":"ref13","first-page":"417","article-title":"IncreasedHIV-1vaccine efficacyagainst viruseswith genetic signatures in Env V2","volume":"490","author":"M Rolland","year":"2012","journal-title":"Nature. Nature Publishing Group"},{"key":"ref14","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"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"12623","DOI":"10.1128\/JVI.01705-14","article-title":"Impact of Clade, Geography and Age of the Epidemic on Hiv-1 Neutralization By Antibodies","volume":"88","author":"P Hraber","year":"2014","journal-title":"J Virol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1128\/JVI.02108-09","article-title":"Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies","volume":"84","author":"MS Seaman","year":"2010","journal-title":"J Virol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"13232","DOI":"10.1128\/JVI.78.23.13232-13252.2004","article-title":"Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies","volume":"78","author":"JM Binley","year":"2004","journal-title":"J Virol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1128\/jvi.76.5.2233-2244.2002","article-title":"Regional clustering of shared neutralization determinants on primary isolates of clade C human immunodeficiency virus type 1 from South Africa","volume":"76","author":"R Bures","year":"2002","journal-title":"J Virol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"11776","DOI":"10.1128\/JVI.01730-06","article-title":"Genetic and neutralization properties of subtype C human immunodeficiency virus type 1 molecular env clones from acute and early heterosexually acquired infections in Southern Africa","volume":"80","author":"M Li","year":"2006","journal-title":"J Virol"},{"key":"ref20","first-page":"991","article-title":"Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level","volume":"16","author":"EM Bunnik","year":"2010","journal-title":"Nat Med. Nature Publishing Group"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e1003477","DOI":"10.1371\/journal.ppat.1003477","article-title":"Evidence for a continuous drift of the HIV-1 species towards higher resistance to neutralizing antibodies over the course of the epidemic","volume":"9","author":"M Bouvin-Pley","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"13910","DOI":"10.1128\/JVI.02083-14","article-title":"Drift of the HIV-1 Envelope Glycoprotein gp120 toward Increased Neutralization Resistance over the Course of the Epidemic: a Comprehensive Study Using the Most Potent and Broadly Neutralizing Monoclonal Antibodies","volume":"88","author":"M Bouvin-Pley","year":"2014","journal-title":"J Virol"},{"key":"ref23","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"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"4933","DOI":"10.1093\/nar\/20.18.4933","article-title":"Efficient amplification of HIV half-genomes from tissue DNA","volume":"20","author":"PF Edmonson","year":"1992","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"403","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 Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experie","volume":"43","author":"S Palmer","year":"2005","journal-title":"J Clin Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"5840","DOI":"10.1128\/JVI.64.12.5840-5850.1990","article-title":"Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1","volume":"64","author":"P Simmonds","year":"1990","journal-title":"J Virol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1007\/978-1-59745-170-3_26","article-title":"Measuring HIV neutralization in a luciferase reporter gene assay","volume":"485","author":"DC Montefiori","year":"2009","journal-title":"Methods Mol Biol. United States"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.jim.2013.11.022","article-title":"Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1","volume":"409","author":"M Sarzotti-Kelsoe","year":"2014","journal-title":"J Immunol Methods. Elsevier B.V"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1038\/nbt1371","article-title":"Bioinformatics prediction of HIV coreceptor usage","volume":"25","author":"T Lengauer","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e60566","DOI":"10.1371\/journal.pone.0060566","article-title":"HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRRF01_AE and CRF02_AG","volume":"8","author":"M Mulinge","year":"2013","journal-title":"PLoS One"},{"key":"ref31","first-page":"13376","article-title":"Improved Coreceptor Usage Prediction and Genotypic Monitoring of R5-to-X4 Transition by Motif Analysis of Human Immunodeficiency","volume":"77","author":"MA Jensen","year":"2003","journal-title":"Improved Coreceptor Usage Prediction and Genotypic Monitoring of R5-to-X4 Transition by Motif Analysis of Human Immunodeficiency"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"4698","DOI":"10.1128\/JVI.80.10.4698-4704.2006","article-title":"A Reliable Phenotype Predictor for Human Immunodeficiency Virus Type 1 Subtype C Based on Envelope V3 Sequences \u2020","volume":"80","author":"MA Jensen","year":"2006","journal-title":"J Virol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2334-12-203","article-title":"Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C viruses","volume":"12","author":"S Crous","year":"2012","journal-title":"BMC Infect Dis. BMC Infectious Diseases"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1128\/AAC.00853-06","article-title":"Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism","volume":"51","author":"JM Whitcomb","year":"2007","journal-title":"Antimicrob Agents Chemother"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e255","DOI":"10.1371\/journal.pmed.0030255","article-title":"Insensitivity of paediatric HIV-1 subtype C viruses to broadly neutralising monoclonal antibodies raised against subtype B","volume":"3","author":"ES Gray","year":"2006","journal-title":"PLoS Med"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"10108","DOI":"10.1128\/JVI.79.16.10108-10125.2005","article-title":"Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies","volume":"79","author":"M Li","year":"2005","journal-title":"J Virol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.virol.2005.05.027","article-title":"Use of alternate coreceptors on primary cells by two HIV-1 isolates","volume":"339","author":"T Cilliers","year":"2005","journal-title":"Virology"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1093\/bioinformatics\/17.5.415","article-title":"Retrieval and on-the-fly alignment of sequence fragments from the HIV database","volume":"17","author":"B Gaschen","year":"2001","journal-title":"Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"S Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1089\/aid.1995.11.1413","article-title":"A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences","volume":"11","author":"AC Siepel","year":"1995","journal-title":"AIDS Res Hum Retroviruses. UNITED STATES"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"W634","DOI":"10.1093\/nar\/gkp455","article-title":"A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences","volume":"37","author":"LCJ Alcantara","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"W647","DOI":"10.1093\/nar\/gkp371","article-title":"jpHMM: improving the reliability of recombination prediction in HIV-1","volume":"37","author":"A-K Schultz","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"MN Price","year":"2009","journal-title":"Mol Biol Evol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"405","DOI":"10.2144\/000113370","article-title":"DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites","volume":"48","author":"W Deng","year":"2010","journal-title":"Biotechniques"},{"key":"ref45","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"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"e503","DOI":"10.1371\/journal.pone.0000503","article-title":"HIV-specific probabilistic models of protein evolution","volume":"2","author":"DC Nickle","year":"2007","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.epidem.2009.10.003","article-title":"The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data","volume":"1","author":"I Maljkovic Berry","year":"2009","journal-title":"Epidemics. Elsevier B.V"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"e1000955","DOI":"10.1371\/journal.pcbi.1000955","article-title":"Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies","volume":"6","author":"S Gnanakaran","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"10103","DOI":"10.1128\/JVI.79.16.10103-10107.2005","article-title":"Recommendations for the design and use of standard virus panels to assess neutralizing antibody responses elicited by candidate human immunodeficiency virus type 1 vaccines","volume":"79","author":"JR Mascola","year":"2005","journal-title":"J Virol"},{"key":"ref50","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"},{"key":"ref51","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"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/j.chom.2015.08.006","article-title":"Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses","volume":"18","author":"MA Moody","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1128\/JVI.03136-14","article-title":"Improving Neutralization Potency and Breadth by Combining Broadly Reactive HIV-1 Antibodies Targeting Major Neutralization Epitopes","volume":"89","author":"R Kong","year":"2015","journal-title":"J Virol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e1000598","DOI":"10.1371\/journal.ppat.1000598","article-title":"Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection","volume":"5","author":"PL Moore","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"9586","DOI":"10.1128\/JVI.00141-06","article-title":"Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity","volume":"80","author":"M Sagar","year":"2006","journal-title":"J Virol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"6986","DOI":"10.1128\/JVI.00268-11","article-title":"Longer V1V2 region with increased number of potential N-linked glycosylation sites in the HIV-1 envelope glycoprotein protects against HIV-specific neutralizing antibodies","volume":"85","author":"MJ van Gils","year":"2011","journal-title":"J Virol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"236ra63","DOI":"10.1126\/scitranslmed.3008104","article-title":"Promiscuous Glycan Site Recognition by Antibodies to the High-Mannose Patch of gp120 Broadens Neutralization of HIV","volume":"6","author":"D Sok","year":"2014","journal-title":"Sci Transl Med"},{"key":"ref58","first-page":"466","article-title":"Broad neutralization coverage of HIV by multiple highly potent antibodies","volume":"477","author":"LM Walker","year":"2011","journal-title":"Nature. Nature Publishing Group"},{"key":"ref59","first-page":"1","article-title":"Evolution of an HIV glycan\u2014dependent broadly neutralizing antibody epitope through immune escape","volume":"18","author":"PL Moore","year":"2012","journal-title":"Nat Med. Nature Publishing Group"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1213256","article-title":"A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield","volume":"334","author":"R Pejchal","year":"2011","journal-title":"Science"},{"key":"ref61","first-page":"74","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. Nature Publishing Group"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/nature13601","article-title":"Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface","volume":"515","author":"J Huang","year":"2014","journal-title":"Nature"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"5651","DOI":"10.1128\/JVI.78.11.5651-5657.2004","article-title":"Increased sensitivity to CD4 binding site-directed neutralization following in vitro propagation on primary lymphocytes of a neutralization-resistant human immunodeficiency virus IIIB strain isolated from an accidentally infected laboratory worker","volume":"78","author":"T Beaumont","year":"2004","journal-title":"J Virol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"e1001228","DOI":"10.1371\/journal.ppat.1001228","article-title":"HIV-1 envelope subregion length variation during disease progression","volume":"6","author":"ME Curlin","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1086\/386333","article-title":"Brief but efficient: acute HIV infection and the sexual transmission of HIV","volume":"189","author":"CD Pilcher","year":"2004","journal-title":"J Infect Dis"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1086\/429411","article-title":"Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda","volume":"191","author":"MJ Wawer","year":"2005","journal-title":"J Infect Dis"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"9475","DOI":"10.1128\/JVI.71.12.9475-9481.1997","article-title":"Identification of the V1 region as a linear neutralizing epitope of the simian immunodeficiency virus SIVmac envelope glycoprotein","volume":"71","author":"E Jurkiewicz","year":"1997","journal-title":"J Virol"},{"key":"ref68","first-page":"5205","article-title":"The V1 \/ V2 Domain of gp120 Is a Global Regulator of the Sensitivity of Primary Human Immunodeficiency Virus Type 1 Isolates to Neutralization by Antibodies Commonly Induced upon Infection","volume":"78","author":"A Pinter","year":"2004","journal-title":"The V1 \/ V2 Domain of gp120 Is a Global Regulator of the Sensitivity of Primary Human Immunodeficiency Virus Type 1 Isolates to Neutralization by Antibodies Commonly Induced upon Infection"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"5211","DOI":"10.1128\/JVI.00201-06","article-title":"Evidence for potent autologous neutralizing antibody titers and compact envelopes in early infection with subtype C human immunodeficiency virus type 1","volume":"80","author":"B Li","year":"2006","journal-title":"J Virol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1126\/science.aac5894","article-title":"Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen","volume":"349","author":"JG Jardine","year":"2015","journal-title":"Science (80-)"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"e1005238","DOI":"10.1371\/journal.ppat.1005238","article-title":"A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo","volume":"11","author":"NT Freund","year":"2015","journal-title":"PLOS Pathog"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"e1005520","DOI":"10.1371\/journal.ppat.1005520","article-title":"Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection","volume":"12","author":"K Wagh","year":"2016","journal-title":"PLOS Pathog"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1006641","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2017,9,25]],"date-time":"2017-09-25T00:00:00Z","timestamp":1506297600000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1005742","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,24]],"date-time":"2020-09-24T03:44:45Z","timestamp":1600919085000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1005742"}},"subtitle":[],"editor":[{"given":"Richard A.","family":"Koup","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,7,19]]},"references-count":72,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2016,7,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1005742","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.ppat.1006641","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,19]]}}}