{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T21:58:18Z","timestamp":1768255098186,"version":"3.49.0"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2016,3,31]],"date-time":"2016-03-31T00:00:00Z","timestamp":1459382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0152499","type":"journal-article","created":{"date-parts":[[2016,3,31]],"date-time":"2016-03-31T17:51:14Z","timestamp":1459446674000},"page":"e0152499","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":30,"title":["Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors"],"prefix":"10.1371","volume":"11","author":[{"given":"Rodrigo","family":"Pess\u00f4a","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paula","family":"Loureiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Esther Lopes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna B. F.","family":"Carneiro-Proietti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ester C","family":"Sabino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael P.","family":"Busch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabri S","family":"Sanabani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2016,3,31]]},"reference":[{"issue":"5463","key":"ref1","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":"15","key":"ref2","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1056\/NEJMra0706737","article-title":"The challenge of HIV-1 subtype diversity","volume":"358","author":"BS Taylor","year":"2008","journal-title":"N Engl J Med"},{"issue":"Suppl 1","key":"ref3","doi-asserted-by":"crossref","first-page":"e4","DOI":"10.4081\/idr.2013.s1.e4","article-title":"Current Trends of HIV Recombination Worldwide","volume":"5","author":"KA Lau","year":"2013","journal-title":"Infect Dis Rep"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S0065-3527(08)60343-7","article-title":"Human immunodeficiency viruses in the developing world","volume":"53","author":"M Essex","year":"1999","journal-title":"Adv Virus Res"},{"issue":"9","key":"ref5","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1093\/aje\/152.9.814","article-title":"Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus","volume":"152","author":"C Kuiken","year":"2000","journal-title":"Am J Epidemiol"},{"issue":"8","key":"ref6","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/S1473-3099(02)00343-2","article-title":"Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy","volume":"2","author":"MM Thomson","year":"2002","journal-title":"Lancet Infect Dis"},{"issue":"Suppl 1","key":"ref7","doi-asserted-by":"crossref","first-page":"S24","DOI":"10.1002\/jmv.20603","article-title":"HIV global surveillance: foundation for retroviral discovery and assay development","volume":"78","author":"CA Brennan","year":"2006","journal-title":"J Med Virol"},{"issue":"6","key":"ref8","doi-asserted-by":"crossref","first-page":"e39819","DOI":"10.1371\/journal.pone.0039819","article-title":"Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C","volume":"7","author":"U Neogi","year":"2012","journal-title":"PLoS One"},{"issue":"10","key":"ref9","doi-asserted-by":"crossref","first-page":"5351","DOI":"10.1128\/JVI.02370-12","article-title":"Emergence in Japan of an HIV-1 variant associated with transmission among men who have sex with men (MSM) in China: first indication of the International Dissemination of the Chinese MSM lineage","volume":"87","author":"M Kondo","year":"2013","journal-title":"J Virol"},{"issue":"11","key":"ref10","doi-asserted-by":"crossref","first-page":"e443","DOI":"10.1371\/journal.pmed.0030443","article-title":"Dominance of HIV-1 subtype CRF01_AE in sexually acquired cases leads to a new epidemic in Yunnan province of China","volume":"3","author":"Y Zhang","year":"2006","journal-title":"PLoS Med"},{"issue":"5","key":"ref11","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1111\/j.1537-2995.2011.03415.x","article-title":"The human immunodeficiency virus-1 genotype diversity and drug resistance mutations profile of volunteer blood donors from Chinese blood centers","volume":"52","author":"P Zeng","year":"2012","journal-title":"Transfusion"},{"issue":"5","key":"ref12","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.jinf.2012.10.026","article-title":"Implications of HIV diversity for the HIV-1 pandemic","volume":"66","author":"J Hemelaar","year":"2013","journal-title":"J Infect"},{"issue":"5","key":"ref13","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.meegid.2006.01.003","article-title":"Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in Sao Paulo, Brazil","volume":"6","author":"S Sanabani","year":"2006","journal-title":"Infect Genet Evol"},{"issue":"2","key":"ref14","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1089\/aid.2006.22.171","article-title":"Full-length genome analysis of human immunodeficiency virus type 1 subtype C in Brazil","volume":"22","author":"S Sanabani","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"10","key":"ref15","doi-asserted-by":"crossref","first-page":"e25869","DOI":"10.1371\/journal.pone.0025869","article-title":"Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in Sao Paulo, Brazil","volume":"6","author":"SS Sanabani","year":"2011","journal-title":"PLoS One"},{"issue":"5","key":"ref16","doi-asserted-by":"crossref","first-page":"e62552","DOI":"10.1371\/journal.pone.0062552","article-title":"Variability of HIV-1 genomes among children and adolescents from Sao Paulo, Brazil","volume":"8","author":"SS Sanabani","year":"2013","journal-title":"PLoS One"},{"key":"ref17","article-title":"Enhanced detection of viral diversity using partial and near full-length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil","author":"R Pessoa","year":"2014","journal-title":"Transfusion"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1097\/QAI.0b013e31828ff979","article-title":"HIV genotypes and primary drug resistance among HIV-seropositive blood donors in Brazil: role of infected blood donors as sentinel populations for molecular surveillance of HIV","volume":"63","author":"CS Alencar","year":"2013","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"3","key":"ref19","doi-asserted-by":"crossref","first-page":"e93374","DOI":"10.1371\/journal.pone.0093374","article-title":"Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology","volume":"9","author":"R Pessoa","year":"2014","journal-title":"PLoS One"},{"issue":"14","key":"ref20","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"ref21","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1089\/aid.1995.11.1423","article-title":"Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning","volume":"11","author":"MO Salminen","year":"1995","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"1","key":"ref22","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"KS Lole","year":"1999","journal-title":"J Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1471-2105-7-265","article-title":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes","volume":"7","author":"AK Schultz","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"ref24","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":"12","key":"ref25","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"},{"issue":"11","key":"ref26","doi-asserted-by":"crossref","first-page":"e112674","DOI":"10.1371\/journal.pone.0112674","article-title":"Deep sequencing of HIV-1 near full-length proviral genomes identifies high rates of BF1 recombinants including two novel circulating recombinant forms (CRF) 70_BF1 and a disseminating 71_BF1 among blood donors in Pernambuco, Brazil","volume":"9","author":"R Pessoa","year":"2014","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/1471-2334-10-224","article-title":"Prevalence, estimated HIV-1 incidence and viral diversity among people seeking voluntary counseling and testing services in Rio de Janeiro, Brazil","volume":"10","author":"CA de Castro","year":"2010","journal-title":". BMC Infect Dis"},{"issue":"7","key":"ref28","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1590\/S0074-02762007005000109","article-title":"Antiretroviral resistance in individuals presenting therapeutic failure and subtypes of the human immunodeficiency virus type 1 in the Northeast Region of Brazil","volume":"102","author":"AM Cavalcanti","year":"2007","journal-title":"Mem Inst Oswaldo Cruz"},{"issue":"1","key":"ref29","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1097\/00042560-199901010-00009","article-title":"HIV-1 subtypes among blood donors from Rio de Janeiro, Brazil","volume":"20","author":"A Tanuri","year":"1999","journal-title":"J Acquir Immune Defic Syndr Hum Retrovirol"},{"issue":"3","key":"ref30","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1097\/01.qai.0000199097.88344.50","article-title":"Trends in antiretroviral drug resistance and clade distributions among HIV-1\u2014infected blood donors in Sao Paulo, Brazil","volume":"41","author":"CC Barreto","year":"2006","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1742-4690-7-39","article-title":"HIV-1 recombinants with multiple parental strains in low-prevalence, remote regions of Cameroon: evolutionary relics?","volume":"7","author":"JK Carr","year":"2010","journal-title":"Retrovirology"},{"issue":"7","key":"ref32","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1089\/aid.2006.22.599","article-title":"Frequency of HIV type 1 dual infection and HIV diversity: analysis of low- and high-risk populations in Mbeya Region, Tanzania","volume":"22","author":"KH Herbinger","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"15","key":"ref33","doi-asserted-by":"crossref","first-page":"2055","DOI":"10.1097\/00002030-200210180-00011","article-title":"Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay","volume":"16","author":"M Hoelscher","year":"2002","journal-title":"AIDS"},{"issue":"4","key":"ref34","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1093\/infdis\/171.4.805","article-title":"Dual infection with human immunodeficiency virus type 1 of distinct envelope subtypes in humans","volume":"171","author":"AW Artenstein","year":"1995","journal-title":"J Infect Dis"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1086\/517360","article-title":"Horizontal and vertical transmission of human immunodeficiency virus type 1 dual infections caused by viruses of subtypes B and C","volume":"177","author":"LM Janini","year":"1998","journal-title":"J Infect Dis"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/1743-422X-9-223","article-title":"Frequency of subtype B and F1 dual infection in HIV-1 positive, Brazilian men who have sex with men","volume":"9","author":"AC Soares de Oliveira","year":"2012","journal-title":"Virol J"},{"issue":"1","key":"ref37","doi-asserted-by":"crossref","first-page":"65","DOI":"10.3201\/eid0501.990108","article-title":"Dual and recombinant infections: an integral part of the HIV-1 epidemic in Brazil","volume":"5","author":"A Ramos","year":"1999","journal-title":"Emerg Infect Dis"},{"issue":"11","key":"ref38","doi-asserted-by":"crossref","first-page":"e177","DOI":"10.1371\/journal.ppat.0030177","article-title":"Chronic HIV-1 infection frequently fails to protect against superinfection","volume":"3","author":"A Piantadosi","year":"2007","journal-title":"PLoS Pathog"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0152499","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,18]],"date-time":"2020-09-18T01:09:46Z","timestamp":1600391386000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0152499"}},"subtitle":[],"editor":[{"given":"Lars","family":"Kaderali","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,3,31]]},"references-count":38,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,3,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0152499","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,31]]}}}