{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T17:01:33Z","timestamp":1790182893906,"version":"4.1.0"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2013,9,9]],"date-time":"2013-09-09T00:00:00Z","timestamp":1378684800000},"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.0072448","type":"journal-article","created":{"date-parts":[[2013,9,9]],"date-time":"2013-09-09T22:38:22Z","timestamp":1378766302000},"page":"e72448","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":25,"title":["Phylodynamics of the HIV-1 Epidemic in Cuba"],"prefix":"10.1371","volume":"8","author":[{"given":"Edson","family":"Delatorre","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Bello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,9,9]]},"reference":[{"key":"ref1","first-page":"210","article-title":"Molecular epidemiology of HIV-1 variants in the global AIDS pandemic: an update","volume":"7","author":"MM Thomson","year":"2005","journal-title":"AIDS Rev"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1097\/00002030-200208160-00010","article-title":"High HIV-1 genetic diversity in Cuba","volume":"16","author":"MT Cuevas","year":"2002","journal-title":"Aids"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1089\/aid.2006.22.724","article-title":"HIV Type 1 molecular epidemiology in cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms","volume":"22","author":"L Perez","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/j.jcv.2012.08.019","article-title":"High frequency of antiviral drug resistance and non-B subtypes in HIV-1 patients failing antiviral therapy in Cuba","volume":"55","author":"V Kouri","year":"2012","journal-title":"J Clin Virol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1089\/aid.2011.0295","article-title":"HIV type 1 genetic diversity in newly diagnosed Cuban patients","volume":"28","author":"LY Machado","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1089\/aid.2012.0183","article-title":"Transmitted HIV type 1 drug resistance in newly diagnosed Cuban patients","volume":"29","author":"LY Machado","year":"2013","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.meegid.2013.02.002","article-title":"Antiretroviral drug resistance in HIV-1 therapy-naive patients in Cuba","volume":"16C","author":"L Perez","year":"2013","journal-title":"Infect Genet Evol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1097\/01.aids.0000176215.95119.1d","article-title":"Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba","volume":"19","author":"MM Thomson","year":"2005","journal-title":"Aids"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1097\/01.qai.0000186363.27587.c0","article-title":"Identification of a novel HIV-1 circulating ADG intersubtype recombinant form (CRF19_cpx) in Cuba","volume":"40","author":"G Casado","year":"2005","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/j.meegid.2008.05.003","article-title":"Highly divergent subtypes and new recombinant forms prevail in the HIV\/AIDS epidemic in Angola: New insights into the origins of the AIDS pandemic","volume":"9","author":"I Bartolo","year":"2009","journal-title":"Infect Genet Evol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e42996","DOI":"10.1371\/journal.pone.0042996","article-title":"HIV-1 genetic diversity and transmitted drug resistance mutations among patients from the North, Central and South regions of Angola","volume":"7","author":"JM Afonso","year":"2012","journal-title":"PLoS ONE"},{"key":"ref12","first-page":"1227","article-title":"Recombinant viruses and early global HIV-1 epidemic","volume":"10","author":"ML Kalish","year":"2004","journal-title":"Emerg Infect Dis"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"10498","DOI":"10.1128\/JVI.74.22.10498-10507.2000","article-title":"Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa","volume":"74","author":"N Vidal","year":"2000","journal-title":"J Virol"},{"key":"ref14","article-title":"HIV-1 subtypes and recombinants in the Republic of Congo","author":"FR Niama","year":"2006","journal-title":"Infect Genet Evol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1089\/aid.2012.0083","article-title":"Molecular characterization of HIV type 1 in Brazzaville, Republic of Congo, and first data on resistance to antiretroviral drugs","volume":"28","author":"M Pircher","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1089\/aid.2006.22.1036","article-title":"Increasing HIV type 1 polymorphic diversity but no resistance to antiretroviral drugs in untreated patients from Central African Republic: a 2005 study","volume":"22","author":"V Marechal","year":"2006","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1006\/viro.2001.0976","article-title":"The AG recombinant IbNG and novel strains of group M HIV-1 are common in Cameroon","volume":"286","author":"JK Carr","year":"2001","journal-title":"Virology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/S0042-6822(03)00167-3","article-title":"Biological and genetic characteristics of HIV infections in Cameroon reveals dual group M and O infections and a correlation between SI-inducing phenotype of the predominant CRF02_AG variant and disease stage","volume":"310","author":"L Vergne","year":"2003","journal-title":"Virology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"639","DOI":"10.3390\/v2020639","article-title":"The Evolution of HIV-1 Diversity in Rural Cameroon and its Implications in Vaccine Design and Trials","volume":"2","author":"R Powell","year":"2010","journal-title":"Viruses"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1097\/QAI.0b013e318046ea47","article-title":"Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba","volume":"45","author":"M Sierra","year":"2007","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4876","DOI":"10.1093\/nar\/25.24.4876","article-title":"The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools","volume":"25","author":"JD Thompson","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences","volume":"21","author":"T de Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"ref23","unstructured":"Ray SC (1999) Simplot v2.5.0. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/sray.med.som.jhmi.edu\/SCRoftware\/simplot\/\" xlink:type=\"simple\">http:\/\/sray.med.som.jhmi.edu\/SCRoftware\/simplot\/<\/ext-link>. Accessed 2013 July 16."},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: phylogenetic model averaging","volume":"25","author":"D Posada","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"W557","DOI":"10.1093\/nar\/gki352","article-title":"PHYML Online\u2013a web server for fast maximum likelihood-based phylogenetic inference","volume":"33","author":"S Guindon","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1080\/10635150600755453","article-title":"Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative","volume":"55","author":"M Anisimova","year":"2006","journal-title":"Syst Biol"},{"key":"ref28","unstructured":"Rambaut A (2009) FigTree v1.4.0: Tree Figure Drawing Tool. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/\" xlink:type=\"simple\">http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/<\/ext-link>. Accessed 2013 July 16."},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data","volume":"161","author":"AJ Drummond","year":"2002","journal-title":"Genetics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"AJ Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"AJ Drummond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/molbev\/mss084","article-title":"Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty","volume":"29","author":"G Baele","year":"2012","journal-title":"Mol Biol Evol"},{"key":"ref34","unstructured":"Rambaut A, Drummond A (2007) Tracer v1.4. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/\" xlink:type=\"simple\">http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/<\/ext-link>. Accessed 2013 July 16."},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e41904","DOI":"10.1371\/journal.pone.0041904","article-title":"Phylodynamics of HIV-1 Subtype C Epidemic in East Africa","volume":"7","author":"EO Delatorre","year":"2012","journal-title":"PLoS ONE"},{"key":"ref36","unstructured":"UNAIDS (2013) AIDS INFO DATABASE. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/en\/dataanalysis\/datatools\/aidsinfo\/\" xlink:type=\"simple\">http:\/\/www.unaids.org\/en\/dataanalysis\/datatools\/aidsinfo\/<\/ext-link>. Accessed 2013 July 16."},{"key":"ref37","doi-asserted-by":"crossref","first-page":"18566","DOI":"10.1073\/pnas.0705329104","article-title":"The emergence of HIV\/AIDS in the Americas and beyond","volume":"104","author":"MT Gilbert","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"6359","DOI":"10.1128\/JVI.77.11.6359-6366.2003","article-title":"U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains","volume":"77","author":"KE Robbins","year":"2003","journal-title":"J Virol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e27489","DOI":"10.1371\/journal.pone.0027489","article-title":"Reviewing the history of HIV-1: spread of subtype B in the Americas","volume":"6","author":"DM Junqueira","year":"2011","journal-title":"PLoS ONE"},{"key":"ref40","unstructured":"Figueras MA (2001) International Tourism and the Formation of Productive Clusters in the Cuban Economy. Latin American Studies Association (LASA) XXII Congress, Washington, DC Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www3.dogus.edu.tr\/memek\/DersNotlari\/TOUR%20229\/TOUR%20229-2004%20fall\/cuba_contribution.pdf\" xlink:type=\"simple\">http:\/\/www3.dogus.edu.tr\/memek\/DersNotlari\/TOUR%20229\/TOUR%20229-2004%20fall\/cuba_contribution.pdf<\/ext-link>. Accessed 2013 July 16."},{"key":"ref41","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1097\/00002030-200102160-00023","article-title":"On the recent sharp increase in HIV detections in Cuba","volume":"15","author":"YH Hsieh","year":"2001","journal-title":"AIDS"},{"key":"ref42","unstructured":"UNAIDS (2012) Country progress reports. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/en\/dataanalysis\/knowyourresponse\/countryprogressreports\/2012countries\/ce_CU_Narrative_Report\" xlink:type=\"simple\">http:\/\/www.unaids.org\/en\/dataanalysis\/knowyourresponse\/countryprogressreports\/2012countries\/ce_CU_Narrative_Report<\/ext-link>[1]pdf. Accessed 2013 July 16."},{"key":"ref43","doi-asserted-by":"crossref","first-page":"563","DOI":"10.2105\/AJPH.81.5.563","article-title":"Cuba&apos;s response to the HIV epidemic","volume":"81","author":"EJ Perez-Stable","year":"1991","journal-title":"Am J Public Health"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1080\/01459740.2001.9966178","article-title":"From quarantine to condoms: shifting policies and problems of HIV control in Cuba","volume":"19","author":"H Hansen","year":"2001","journal-title":"Med Anthropol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/1471-2334-7-130","article-title":"The HIV\/AIDS epidemic in Cuba: description and tentative explanation of its low HIV prevalence","volume":"7","author":"H de Arazoza","year":"2007","journal-title":"BMC Infect Dis"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1590\/S1020-49892009000700012","article-title":"HIV\/AIDS in Cuba: lessons and challenges","volume":"26","author":"T Anderson","year":"2009","journal-title":"Rev Panam Salud Publica"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1007\/s00239-004-0206-5","article-title":"Different epidemic potentials of the HIV-1B and C subtypes","volume":"60","author":"M Salemi","year":"2005","journal-title":"J Mol Evol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.meegid.2006.11.002","article-title":"Demographic history of HIV-1 subtypes B and F in Brazil","volume":"7","author":"G Bello","year":"2007","journal-title":"Infect Genet Evol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1089\/aid.2009.0106","article-title":"Short communication: Evidences of recent decline in the expansion rate of the HIV type 1 subtype C and CRF31_BC epidemics in southern Brazil","volume":"25","author":"G Bello","year":"2009","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1742-4690-7-22","article-title":"Phylodynamics of HIV-1 circulating recombinant forms 12_BF and 38_BF in Argentina and Uruguay","volume":"7","author":"G Bello","year":"2010","journal-title":"Retrovirology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e17485","DOI":"10.1371\/journal.pone.0017485","article-title":"Analysis of the origin and evolutionary history of HIV-1 CRF28_BF and CRF29_BF reveals a decreasing prevalence in the AIDS epidemic of Brazil","volume":"6","author":"N Ristic","year":"2011","journal-title":"PLoS ONE"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.meegid.2012.03.014","article-title":"Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania","volume":"12","author":"G Bello","year":"2012","journal-title":"Infect Genet Evol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"4425","DOI":"10.1073\/pnas.0407534102","article-title":"Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups","volume":"102","author":"S Hue","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e1390","DOI":"10.1371\/journal.pone.0001390","article-title":"High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania","volume":"3","author":"M Salemi","year":"2008","journal-title":"PLoS ONE"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1097\/QAI.0b013e3181eb3002","article-title":"Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy","volume":"55","author":"G Zehender","year":"2010","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.meegid.2004.06.011","article-title":"Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth","volume":"5","author":"PR Walker","year":"2005","journal-title":"Infect Genet Evol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1097\/QAD.0b013e32833999e1","article-title":"Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia","volume":"24","author":"DC Tully","year":"2010","journal-title":"Aids"},{"key":"ref58","article-title":"Spatiotemporal dynamics of the HIV-1 CRF06_cpx epidemic in western Africa","author":"E Delatorre","year":"2013","journal-title":"Aids"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"e25286","DOI":"10.1371\/journal.pone.0025286","article-title":"Phylodynamics of HIV-1 subtype B among the men-having-sex-with-men (MSM) population in Hong Kong","volume":"6","author":"JH Chen","year":"2011","journal-title":"PLoS ONE"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0072448","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T22:28:14Z","timestamp":1646519294000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0072448"}},"subtitle":[],"editor":[{"given":"Chiyu","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,9,9]]},"references-count":59,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2013,9,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0072448","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9,9]]}}}