{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T11:35:19Z","timestamp":1789472119599,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.ppat.1009258","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T00:00:00Z","timestamp":1614211200000}}],"reference-count":64,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T00:00:00Z","timestamp":1613088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Mega-projects of National Science Research for the 13th Five-Year Plan","award":["2017ZX10201101"],"award-info":[{"award-number":["2017ZX10201101"]}]},{"name":"Mega-projects of National Science Research for the 13th Five-Year Plan","award":["2018ZX10721102006003"],"award-info":[{"award-number":["2018ZX10721102006003"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81871637"],"award-info":[{"award-number":["81871637"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected\/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE\/CRF07_BC superinfected putative donor and diverse CRF01_AE\/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on<jats:italic>env<\/jats:italic>, and shared 4\u20137 breakpoints with each other. Moreover, 3\u2019 half-genomes of recombinant strains from five recipients had identical\/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.<\/jats:p>","DOI":"10.1371\/journal.ppat.1009258","type":"journal-article","created":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T21:57:10Z","timestamp":1613167030000},"page":"e1009258","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients"],"prefix":"10.1371","volume":"17","author":[{"given":"Yang","family":"Gao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minghui","family":"An","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haibo","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenxing","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5333-8943","authenticated-orcid":true,"given":"Hong","family":"Shang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1427-8428","authenticated-orcid":true,"given":"Xiaoxu","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,12]]},"reference":[{"issue":"1\u20132","key":"ppat.1009258.ref001","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.virusres.2008.01.007","article-title":"Implications of recombination for HIV diversity","volume":"134","author":"BC Ramirez","year":"2008","journal-title":"Virus research"},{"issue":"5463","key":"ppat.1009258.ref002","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 nomenclature proposal","volume":"288","author":"DL Robertson","year":"2000","journal-title":"Science"},{"issue":"3","key":"ppat.1009258.ref003","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.molmed.2011.12.001","article-title":"The origin and diversity of the HIV-1 pandemic","volume":"18","author":"J. 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Online Context of Sex Seeking Among Men Who Have Sex With Men in China","volume":"44","author":"B Cao","year":"2017","journal-title":"Sex Transm Dis."},{"issue":"5","key":"ppat.1009258.ref031","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1177\/0956462417738468","article-title":"Relationship between the use of gay mobile phone applications and HIV infection among men who have sex with men in Ningbo, China: a cross-sectional study","volume":"29","author":"H Hong","year":"2018","journal-title":"International journal of STD & AIDS"},{"issue":"4","key":"ppat.1009258.ref032","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1136\/sextrans-2013-051332","article-title":"Internet-based partner selection and risk for unprotected anal intercourse in sexual encounters among men who have sex with men: a meta-analysis of observational studies","volume":"90","author":"JA Lewnard","year":"2014","journal-title":"Sex Transm Infect"},{"issue":"10","key":"ppat.1009258.ref033","doi-asserted-by":"crossref","first-page":"2222","DOI":"10.1007\/s10461-016-1371-4","article-title":"Seeking Male Sexual Partners via Internet and Traditional Venues among Chinese Men Who Have Sex with Men: Implications for HIV Risk Reduction Interventions","volume":"20","author":"Y Liu","year":"2016","journal-title":"AIDS Behav."},{"issue":"1","key":"ppat.1009258.ref034","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1089\/apc.2011.0153","article-title":"A systematic review of behavioral and treatment outcome studies among HIV-infected men who have sex with men who abuse crystal methamphetamine","volume":"26","author":"R Rajasingham","year":"2012","journal-title":"AIDS Patient Care STDS"},{"issue":"8","key":"ppat.1009258.ref035","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":"Journal of virology"},{"key":"ppat.1009258.ref036","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1471-2148-6-10","article-title":"Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1","volume":"6","author":"CTT Edwards","year":"2006","journal-title":"BMC Evol Biol"},{"issue":"5048","key":"ppat.1009258.ref037","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":"3","key":"ppat.1009258.ref038","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1097\/COH.0000000000000536","article-title":"Phylogenetics in HIV transmission: taking within-host diversity into account","volume":"14","author":"T. Leitner","year":"2019","journal-title":"Current opinion in HIV and AIDS"},{"issue":"10","key":"ppat.1009258.ref039","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1073\/pnas.1522930113","article-title":"Phylogenetically resolving epidemiologic linkage","volume":"113","author":"EO Romero-Severson","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"ppat.1009258.ref040","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1089\/088922203322230923","article-title":"A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand","volume":"19","author":"S Tovanabutra","year":"2003","journal-title":"AIDS research and human retroviruses"},{"issue":"1","key":"ppat.1009258.ref041","article-title":"Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF55_01B, Identified in China","volume":"1","author":"X Han","year":"2013","journal-title":"Genome Announc."},{"issue":"6","key":"ppat.1009258.ref042","doi-asserted-by":"crossref","first-page":"e99693","DOI":"10.1371\/journal.pone.0099693","article-title":"Identification and characterization of a novel HIV-1 circulating recombinant form (CRF59_01B) identified among men-who-have-sex-with-men in China","volume":"9","author":"W Zhang","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"ppat.1009258.ref043","doi-asserted-by":"crossref","first-page":"e54322","DOI":"10.1371\/journal.pone.0054322","article-title":"New emerging recombinant HIV-1 strains and close transmission linkage of HIV-1 strains in the Chinese MSM population indicate a new epidemic risk","volume":"8","author":"J Wu","year":"2013","journal-title":"PLoS One"},{"key":"ppat.1009258.ref044","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.meegid.2019.04.024","article-title":"Genetic characterization and recombinant history of a novel HIV-1 circulating recombinant form (CRF101_01B) identified in 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Zhi."},{"issue":"6","key":"ppat.1009258.ref055","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1056\/NEJMoa1105243","article-title":"Prevention of HIV-1 infection with early antiretroviral therapy","volume":"365","author":"MS Cohen","year":"2011","journal-title":"N Engl J Med."},{"key":"ppat.1009258.ref056","doi-asserted-by":"crossref","first-page":"2322","DOI":"10.3389\/fimmu.2018.02322","article-title":"The Early Antibody-Dependent Cell-Mediated Cytotoxicity Response Is Associated With Lower Viral Set Point in Individuals With Primary HIV Infection","volume":"9","author":"X Chen","year":"2018","journal-title":"Front Immunol."},{"key":"ppat.1009258.ref057","first-page":"725361","article-title":"Recreational drug use among Chinese men who have sex with men: a risky combination with unprotected sex for acquiring HIV infection","volume":"2014","author":"J-J Xu","year":"2014","journal-title":"Biomed Res 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