{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T22:12:32Z","timestamp":1791238352742,"version":"4.1.0"},"reference-count":48,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2014,3,31]],"date-time":"2014-03-31T00:00:00Z","timestamp":1396224000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0093374","type":"journal-article","created":{"date-parts":[[2014,3,31]],"date-time":"2014-03-31T20:30:53Z","timestamp":1396297853000},"page":"e93374","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":42,"title":["Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology"],"prefix":"10.1371","volume":"9","author":[{"given":"Rodrigo","family":"Pess\u00f4a","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaqueline Tomoko","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youko","family":"Nukui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana","family":"Pereira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Kasseb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Augusto C\u00e9sar","family":"Penalva de Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aluisio Cotrim","family":"Segurado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabri Saeed","family":"Sanabani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,3,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1016\/S0140-6736(85)92734-5","article-title":"Antibodies to human T-lymphotropic virus type-I in patients with tropical spastic paraparesis","volume":"2","author":"A Gessain","year":"1985","journal-title":"Lancet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1016\/S0140-6736(86)91298-5","article-title":"HTLV-I associated myelopathy, a new clinical entity","volume":"1","author":"M Osame","year":"1986","journal-title":"Lancet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"7415","DOI":"10.1073\/pnas.77.12.7415","article-title":"Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma","volume":"77","author":"BJ Poiesz","year":"1980","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1073\/pnas.79.6.2031","article-title":"Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease","volume":"79","author":"M Yoshida","year":"1982","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1016\/0140-6736(92)90702-5","article-title":"Fibroblast growth factor 6 gene expression in AIDS-associated Kaposi's sarcoma","volume":"339","author":"YQ Huang","year":"1992","journal-title":"Lancet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1016\/S0140-6736(87)91362-6","article-title":"T-lymphocyte alveolitis in HTLV-I-associated myelopathy","volume":"2","author":"M Sugimoto","year":"1987","journal-title":"Lancet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.2169\/internalmedicine.31.1213","article-title":"Hashimoto's thyroiditis in HTLV-I carriers","volume":"31","author":"H Kawai","year":"1992","journal-title":"Intern Med"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/S0140-6736(89)90038-X","article-title":"Chronic inflammatory arthropathy associated with HTLV-I","volume":"1","author":"K Nishioka","year":"1989","journal-title":"Lancet"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0736-4679(99)00173-0","article-title":"Global epidemic of human T-cell lymphotropic virus type-I (HTLV-I)","volume":"18","author":"RF Edlich","year":"2000","journal-title":"J Emerg Med"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"5131","DOI":"10.1038\/sj.onc.1206551","article-title":"Human T-cell leukemia virus type I and adult T-cell leukemia","volume":"22","author":"M Matsuoka","year":"2003","journal-title":"Oncogene"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"6058","DOI":"10.1038\/sj.onc.1208968","article-title":"Global epidemiology of HTLV-I infection and associated diseases","volume":"24","author":"FA Proietti","year":"2005","journal-title":"Oncogene"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"388","DOI":"10.3389\/fmicb.2012.00388","article-title":"Epidemiological Aspects and World Distribution of HTLV-1 Infection","volume":"3","author":"A Gessain","year":"2012","journal-title":"Front Microbiol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"3618","DOI":"10.1073\/pnas.80.12.3618","article-title":"Human adult T-cell leukemia virus: complete nucleotide sequence of the provirus genome integrated in leukemia cell DNA","volume":"80","author":"M Seiki","year":"1983","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1007\/BF02983552","article-title":"T-cell control by human T-cell leukemia\/lymphoma virus type 1","volume":"78","author":"G Franchini","year":"2003","journal-title":"Int J Hematol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/S1473-3099(07)70081-6","article-title":"Human T-lymphotropic virus 1: recent knowledge about an ancient infection","volume":"7","author":"K Verdonck","year":"2007","journal-title":"Lancet Infect Dis"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"3655","DOI":"10.1099\/0022-1317-75-12-3655","article-title":"Phylogenetic classification of human T cell leukaemia\/lymphoma virus type I genotypes in five major molecular and geographical subtypes","volume":"75","author":"AU Vidal","year":"1994","journal-title":"J Gen Virol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1099\/0022-1317-79-11-2695","article-title":"Evidence for a post-Columbian introduction of human T-cell lymphotropic virus [type I] [corrected] in Latin America","volume":"79","author":"S Van Dooren","year":"1998","journal-title":"J Gen Virol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1046\/j.1537-2995.1997.37297203532.x","article-title":"Distribution of human T-lymphotropic virus type I among blood donors: a nationwide Brazilian study","volume":"37","author":"B Galvao-Castro","year":"1997","journal-title":"Transfusion"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1089\/aid.2011.0143","article-title":"Human T-lymphotropic virus type 1 and type 2 seroprevalence, incidence, and residual transfusion risk among blood donors in Brazil during 2007-2009","volume":"28","author":"AB Carneiro-Proietti","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1097\/00126334-200312150-00013","article-title":"HTLV-I in the general population of Salvador, Brazil: a city with African ethnic and sociodemographic characteristics","volume":"34","author":"I Dourado","year":"2003","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1590\/S0102-311X2005000300027","article-title":"Heterogeneous geographic distribution of human T-cell lymphotropic viruses I and II (HTLV-I\/II): serological screening prevalence rates in blood donors from large urban areas in Brazil","volume":"21","author":"B Catalan-Soares","year":"2005","journal-title":"Cad Saude Publica"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"8247","DOI":"10.1128\/JVI.00897-09","article-title":"Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques","volume":"83","author":"BN Bimber","year":"2009","journal-title":"J Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"12087","DOI":"10.1128\/JVI.01378-10","article-title":"Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing","volume":"84","author":"BN Bimber","year":"2010","journal-title":"J Virol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e13564","DOI":"10.1371\/journal.pone.0013564","article-title":"Development of a low bias method for characterizing viral populations using next generation sequencing technology","volume":"5","author":"SM Willerth","year":"2010","journal-title":"PLoS One"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e36494","DOI":"10.1371\/journal.pone.0036494","article-title":"Low-cost ultra-wide genotyping using Roche\/454 pyrosequencing for surveillance of HIV drug resistance","volume":"7","author":"DM Dudley","year":"2012","journal-title":"PLoS One"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1101\/gr.6468307","article-title":"Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance","volume":"17","author":"C Wang","year":"2007","journal-title":"Genome Res"},{"key":"ref27","unstructured":"Osame M (1990) Review of WHO Kagoshima Meeting and diagnostic guidelines for HAM\/TSP.In Human Retrovirology: HTLV. Edited by Blattner W. New York: Raven. 191\u2013197."},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1128\/JCM.30.6.1605-1607.1992","article-title":"Sensitive and specific polymerase chain reaction assays for diagnosis of human T-cell lymphotropic virus type I (HTLV-I) and HTLV-II infections in HTLV-I\/II-seropositive individuals","volume":"30","author":"W Heneine","year":"1992","journal-title":"J Clin Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/j.jcv.2011.12.033","article-title":"Design and development of a quantitative real time PCR assay for monitoring of HTLV-1 provirus in whole blood","volume":"53","author":"M Naderi","year":"2012","journal-title":"J Clin Virol"},{"key":"ref30","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"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"F Ronquist","year":"2012","journal-title":"Syst Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/1471-2105-10-356","article-title":"phyloXML: XML for evolutionary biology and comparative genomics","volume":"10","author":"MV Han","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1086\/315897","article-title":"Phylogenetic subgroups of human T cell lymphotropic virus (HTLV) type I in the tax gene and their association with different risks for HTLV-I-associated myelopathy\/tropical spastic paraparesis","volume":"182","author":"Y Furukawa","year":"2000","journal-title":"J Infect Dis"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1089\/aid.2006.22.953","article-title":"Distribution of human T cell lymphotropic virus type 1 (HTLV-1) subtypes in Brazil: genetic characterization of LTR and tax region","volume":"22","author":"S Kashima","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1590\/S0074-02762002000300009","article-title":"Identification of human T-lymphotropic virus type I (HTLV-I) subtypes using restricted fragment length polymorphism in a cohort of asymptomatic carriers and patients with HTLV-I-associated myelopathy\/tropical spastic paraparesis from Sao Paulo, Brazil","volume":"97","author":"AA Segurado","year":"2002","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1089\/aid.2011.0117","article-title":"Phylogenetic and similarity analysis of HTLV-1 isolates from HIV-coinfected patients from the south and southeast regions of Brazil","volume":"28","author":"MC Magri","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1186\/1743-422X-8-535","article-title":"Correlation between LTR point mutations and proviral load levels among human T cell lymphotropic virus type 1 (HTLV-1) asymptomatic carriers","volume":"8","author":"WK Neto","year":"2011","journal-title":"Virol J"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Leitner T (2002) The molecular epidemiology of human viruses. Berlin, Germany: Springer Science and Business Media.","DOI":"10.1007\/978-1-4615-1157-1"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3770","DOI":"10.1128\/JVI.65.7.3770-3778.1991","article-title":"In vivo genomic variability of human T-cell leukemia virus type I depends more upon geography than upon pathologies","volume":"65","author":"F Komurian","year":"1991","journal-title":"J Virol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/310505a0","article-title":"Isolation of HTLV-transformed B-lymphocyte clone from a patient with HTLV-associated adult T-cell leukaemia","volume":"310","author":"DL Longo","year":"1984","journal-title":"Nature"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1128\/JVI.71.2.1317-1333.1997","article-title":"Molecular epidemiology of 58 new African human T-cell leukemia virus type 1 (HTLV-1) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in Pygmies","volume":"71","author":"R Mahieux","year":"1997","journal-title":"J Virol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1097\/01.aids.0000216383.14808.13","article-title":"Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes","volume":"20","author":"LC Alcantara","year":"2006","journal-title":"AIDS"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1089\/aid.2006.0203","article-title":"The close relationship between South African and Latin American HTLV type 1 strains corroborated in a molecular epidemiological study of the HTLV type 1 isolates from a blood donor cohort","volume":"23","author":"AC Mota","year":"2007","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1089\/aid.2008.0024","article-title":"Divergent strains of human T-lymphotropic virus type 1 (HTLV-1) within the Cosmopolitan subtype in Argentina","volume":"24","author":"ME Eirin","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1590\/S0074-02762003000500010","article-title":"Sequence and phylogenetic analysis of human T cell lymphotropic virus type 1 from Tumaco, Colombia","volume":"98","author":"N Balcazar","year":"2003","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"101","DOI":"10.4269\/ajtmh.1995.52.101","article-title":"Sequence and phylogenetic analyses of human T cell lymphotropic virus type 1 from a Brazilian woman with adult T cell leukemia: comparison with virus strains from South America and the Caribbean basin","volume":"52","author":"KJ Song","year":"1995","journal-title":"Am J Trop Med Hyg"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1089\/088922201750237068","article-title":"Phylogenetic characterization of a new HTLV type 1 from the Ainu in Japan","volume":"17","author":"M Yamashita","year":"2001","journal-title":"AIDS Res Hum Retroviruses"}],"updated-by":[{"DOI":"10.1371\/journal.pone.0102223","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2014,7,9]],"date-time":"2014-07-09T00:00:00Z","timestamp":1404864000000}}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0093374","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T02:04:34Z","timestamp":1597629874000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0093374"}},"subtitle":[],"editor":[{"given":"William M.","family":"Switzer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,3,31]]},"references-count":48,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2014,3,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0093374","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pone.0102223","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,3,31]]}}}