{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T06:41:03Z","timestamp":1784011263592,"version":"3.55.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000},"content-version":"vor","delay-in-days":21,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000092","name":"Ontario Genomics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-155990"],"award-info":[{"award-number":["PJT-155990"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-156178"],"award-info":[{"award-number":["PJT-156178"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["FRN-130609"],"award-info":[{"award-number":["FRN-130609"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["BOP-149562"],"award-info":[{"award-number":["BOP-149562"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"DOI":"10.1093\/ve\/vey039","type":"journal-article","created":{"date-parts":[[2018,11,30]],"date-time":"2018-11-30T15:11:36Z","timestamp":1543590696000},"source":"Crossref","is-referenced-by-count":9,"title":["Evidence for a recombinant origin of HIV-1 Group M from genomic variation"],"prefix":"10.1093","volume":"5","author":[{"given":"Abayomi S","family":"Olabode","sequence":"first","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6796-2453","authenticated-orcid":false,"given":"Mariano","family":"Avino","sequence":"additional","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garway T","family":"Ng","sequence":"additional","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faisal","family":"Abu-Sardanah","sequence":"additional","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David W","family":"Dick","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Art F Y","family":"Poon","sequence":"additional","affiliation":[{"name":"Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada"},{"name":"Department of Applied Mathematics, Western University, London, Ontario, Canada"},{"name":"Department of Microbiology & Immunology, Western University, London, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,1,22]]},"reference":[{"key":"key\n\t\t\t\t2019012210583147200_vey039-B1","doi-asserted-by":"crossref","first-page":"8543","DOI":"10.1128\/JVI.00463-07","article-title":"\u2018Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form\u2019","volume":"81","author":"Abecasis","year":"2007","journal-title":"Journal of Virology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B2","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1742-4690-10-49","article-title":"Within-host and between-host Evolutionary Rates across the HIV-1 Genome","volume":"10","author":"Alizon","year":"2013","journal-title":"Retrovirology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B3","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1093\/bioinformatics\/bts181","article-title":"Ranking Viruses: Measures of Positional Importance within Networks Define Core Viruses for Rational Polyvalent Vaccine Development","volume":"28","author":"Anderson","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B4","doi-asserted-by":"crossref","first-page":"e1000178","DOI":"10.1371\/journal.pcbi.1000178","article-title":"Identifying the Important HIV-1 Recombination Breakpoints","volume":"4","author":"Archer","year":"2008","journal-title":"PLoS Computational Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B5","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed Phylogenetics and Dating with Confidence","volume":"4","author":"Drummond","year":"2006","journal-title":"PLoS Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B6","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":"Drummond","year":"2007","journal-title":"BMC Evolutionary Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B7","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s12862-015-0312-6","article-title":"Declining Transition\/transversion Ratios through Time Reveal Limitations to the Accuracy of Nucleotide Substitution Models","volume":"15","author":"Duch\u00eane","year":"2015","journal-title":"BMC Evolutionary Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B8","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1534\/genetics.105.052019","article-title":"Evolution of the HIV-1 Envelope Gene Is Dominated by Purifying Selection","volume":"174","author":"Edwards","year":"2006","journal-title":"Genetics"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B9","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1126\/science.1256739","article-title":"The Early Spread and Epidemic Ignition of HIV-1 in Human Populations","volume":"346","author":"Faria","year":"2014","journal-title":"Science (New York, N.Y.)"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B10","doi-asserted-by":"crossref","first-page":"7013","DOI":"10.1128\/JVI.70.10.7013-7029.1996","article-title":"The Heterosexual Human Immunodeficiency Virus Type 1 Epidemic in Thailand Is Caused by an Intersubtype (A\/E) recombinant of African Origin","volume":"70","author":"Gao","year":"1996","journal-title":"Journal of Virology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B11","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vew003","article-title":"The Effects of Sampling Strategy on the Quality of Reconstruction of Viral Population Dynamics Using Bayesian Skyline Family Coalescent Methods: A Simulation Study","volume":"2","author":"Hall","year":"2016","journal-title":"Virus Evolution"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B12","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":"Hemelaar","year":"2012","journal-title":"Trends in Molecular Medicine"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B13","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1093\/molbev\/msi145","article-title":"Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times","volume":"22","author":"Ho","year":"2005","journal-title":"Molecular Biology and Evolution"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B14","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":"Katoh","year":"2002","journal-title":"Nucleic Acids Research"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B15","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s00357-017-9224-z","article-title":"On the Correspondence between Procrustes Analysis and Bidimensional Regression","volume":"34","author":"Kern","year":"2017","journal-title":"Journal of Classification"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B16","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1128\/JVI.02353-15","article-title":"Population-level Immune-mediated Adaptation in HIV-1 Polymerase during the North American Epidemic","volume":"90","author":"Kinloch","year":"2016","journal-title":"Journal of Virology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B17","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1126\/science.288.5472.1789","article-title":"Timing the Ancestor of the HIV-1 Pandemic Strains","volume":"288","author":"Korber","year":"2000","journal-title":"Science (New York, N.Y.)"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B18","doi-asserted-by":"crossref","first-page":"10752","DOI":"10.1073\/pnas.96.19.10752","article-title":"The Molecular Clock of HIV-1 Unveiled Through Analysis of a Known Transmission History","volume":"96","author":"Leitner","year":"1999","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B19","volume-title":"lsmeans: Least-Squares Means R Package Version 200\u20134","author":"Lenth","year":"2004"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B20","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: A Fast, Unconstrained Bayesian Approximation for Inferring Selection","volume":"30","author":"Murrell","year":"2013","journal-title":"Molecular Biology and Evolution"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B21","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1146\/annurev.genet.35.102401.090551","article-title":"Mechanisms of Retroviral Recombination","volume":"35","author":"Negroni","year":"2001","journal-title":"Annual Review of Genetics"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B22","doi-asserted-by":"crossref","first-page":"e1000660","DOI":"10.1371\/journal.pcbi.1000660","article-title":"Recombination Rate and Selection Strength in HIV Intra-Patient Evolution","volume":"6","author":"Neher","year":"2010","journal-title":"PLoS Computational Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B23","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: Analyses of Phylogenetics and Evolution in R Language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics (Oxford, England)"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B24","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S1473-3099(15)70036-8","article-title":"The PANGEA-HIV Consortium: Phylogenetics and Networks for Generalised HIV Epidemics in Africa","volume":"15","author":"Pillay","year":"2015","journal-title":"The Lancet Infectious Diseases"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B25","doi-asserted-by":"crossref","first-page":"e1000581","DOI":"10.1371\/journal.pcbi.1000581","article-title":"An Evolutionary Model-based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1","volume":"5","author":"Pond","year":"2009","journal-title":"PLoS Computational Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B26","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2013Approximately Maximum-Likelihood Trees for Large Alignments","volume":"5","author":"Price","year":"2010","journal-title":"PloS One"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B27","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 Nomenclature Proposal","volume":"288","author":"Robertson","year":"2000","journal-title":"Science (New York, N.Y.)"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B28","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1089\/aid.2017.0244","article-title":"ARCHITECT HIV Combo Ag\/Ab and RealTime HIV-1 Assays Detect Diverse HIV Strains in Clinical Specimens","volume":"34","author":"Rodgers","year":"2018","journal-title":"AIDS Research and Human Retroviruses"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B29","first-page":"233","article-title":"Coalescent Approaches","author":"Rodrigo","year":"1999","journal-title":"The Evolution of HIV"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B30","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":"Salminen","year":"1995","journal-title":"AIDS Research and Human Retroviruses"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B31","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1093\/genetics\/156.2.879","article-title":"Consequences of Recombination on Traditional Phylogenetic Analysis","volume":"156","author":"Schierup","year":"2000","journal-title":"Genetics"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B32","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511809682","volume-title":"Kernel Methods for Pattern Analysis","author":"Shawe-Taylor","year":"2004"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B33","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":"Siepel","year":"1995","journal-title":"AIDS Research and Human Retroviruses"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B34","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S1473-3099(10)70186-9","article-title":"Tracking a Century of Global Expansion and Evolution of HIV to Drive Understanding and to Combat Disease","volume":"11","author":"Tebit","year":"2011","journal-title":"The Lancet Infectious Diseases"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B35","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/sysbio\/syv068","article-title":"Fast Dating Using Least-squares Criteria and Algorithms","volume":"65","author":"To","year":"2016","journal-title":"Systematic Biology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B36","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/emph\/eov022","article-title":"Near Full-Length HIV Type 1M Genomic Sequences from Cameroon: Evidence of Early Diverging Under-sampled Lineages","volume":"2015","author":"Tongo","year":"2015","journal-title":"Evolution, Medicine, and Public Health"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B37","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1128\/JVI.02302-15","article-title":"High Degree of HIV-1 Group M (HIV-1M) genetic Diversity within Circulating Recombinant Forms: Insight into the Early Events of HIV-1M Evolution","volume":"90","author":"Tongo","year":"2016","journal-title":"Journal of Virology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B38","author":"UNAIDS","year":"2017"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B39","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1089\/aid.2008.0283","article-title":"Genetic Characterization of Eight Full-length HIV Type 1 Genomes from the Democratic Republic of Congo (DRC) reveal a New Subsubtype, A5, in the a Radiation That Predominates in the Recombinant Structure of CRF26_A5U","volume":"25","author":"Vidal","year":"2009","journal-title":"AIDS Research and Human Retroviruses"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B40","doi-asserted-by":"crossref","first-page":"vex032","DOI":"10.1093\/ve\/vex032","article-title":"Divergent HIV-1 Strains (CRF92_C2U and CRF93_cpx) Co-circulating in the Democratic Republic of the Congo: Phylogenetic Insights on the Early Evolutionary History of Subtype C","volume":"3","author":"Villabona Arenas","year":"2017","journal-title":"Virus Evolution"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B41","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.1128\/JVI.02478-12","article-title":"Estimating the Rate of Intersubtype Recombination in Early HIV-1 Group M Strains","volume":"87","author":"Ward","year":"2013","journal-title":"Journal of Virology"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B42","doi-asserted-by":"crossref","first-page":"3355","DOI":"10.1093\/molbev\/msr170","article-title":"Purifying Selection Can Obscure the Ancient Age of Viral Lineages","volume":"28","author":"Wertheim","year":"2011","journal-title":"Molecular Biology and Evolution"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B43","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature07390","article-title":"Direct Evidence of Extensive Diversity of HIV-1 in Kinshasa by 1960","volume":"455","author":"Worobey","year":"2008","journal-title":"Nature"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B44","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1017\/CBO9780511819049.022","article-title":"Assessing Substitution Saturation with DAMBE","author":"Xia","year":"2009","journal-title":"The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B45","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/genetics\/155.1.431","article-title":"Codon-substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites","volume":"155","author":"Yang","year":"2000","journal-title":"Genetics"},{"key":"key\n\t\t\t\t2019012210583147200_vey039-B46","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1742-4690-7-25","article-title":"The Role of Recombination in the Emergence of a Complex and Dynamic HIV Epidemic","volume":"7","author":"Zhang","year":"2010","journal-title":"Retrovirology"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/ve\/article-pdf\/5\/1\/vey039\/27579336\/vey039.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T03:33:43Z","timestamp":1662521623000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/vey039\/5298912"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,1]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,1,22]]},"published-print":{"date-parts":[[2019,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/vey039","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/364075","asserted-by":"object"}]},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,1]]},"published":{"date-parts":[[2019,1,1]]}}}