{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T10:41:25Z","timestamp":1775644885539,"version":"3.50.1"},"reference-count":77,"publisher":"Microbiology Society","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:p>Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial <jats:italic>pol<\/jats:italic> and 248 partial <jats:italic>env<\/jats:italic> sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with C\u00f4te d\u2019Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, C\u00f4te d\u2019Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.<\/jats:p>","DOI":"10.1099\/vir.0.038638-0","type":"journal-article","created":{"date-parts":[[2011,12,22]],"date-time":"2011-12-22T05:10:28Z","timestamp":1324530628000},"page":"889-899","source":"Crossref","is-referenced-by-count":55,"title":["Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A"],"prefix":"10.1099","volume":"93","author":[{"given":"Nuno R.","family":"Faria","sequence":"first","affiliation":[{"name":"Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium"}]},{"given":"Ioannis","family":"Hodges-Mameletzis","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK"}]},{"given":"Joana C.","family":"Silva","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal"}]},{"given":"Berta","family":"Rod\u00e9s","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain"}]},{"given":"Smit","family":"Erasmus","sequence":"additional","affiliation":[{"name":"HPA Birmingham, Heartlands Hospital, Birmingham, UK"}]},{"given":"Stefania","family":"Paolucci","sequence":"additional","affiliation":[{"name":"Fondazione IRCCS Policlinico, San Matteo, Italy"}]},{"given":"Jean","family":"Ruelle","sequence":"additional","affiliation":[{"name":"AIDS Reference Laboratory, Universit\u00e9 Catholique de Louvain, Brussels, Belgium"}]},{"given":"Danuta","family":"Pieniazek","sequence":"additional","affiliation":[{"name":"Incidence and Case Surveillance Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}]},{"given":"Nuno","family":"Taveira","sequence":"additional","affiliation":[{"name":"Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisboa, Portugal"},{"name":"Centro de Investiga\u00e7\u00e3o Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ci\u00eancias da Sa\u00fade Egas Moniz, Monte de Caparica, Portugal"},{"name":"Unidade dos Retrov\u00edrus e Infec\u00e7\u00f5es Associadas, Centro de Patog\u00e9nese Molecular, Faculdade de Farm\u00e1cia de Lisboa, Lisboa, Portugal"}]},{"given":"Ana","family":"Trevi\u00f1o","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain"}]},{"given":"Maria F.","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal"}]},{"given":"Sabelle","family":"Jallow","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK"}]},{"given":"Li","family":"Xu","sequence":"additional","affiliation":[{"name":"HPA Birmingham, Heartlands Hospital, Birmingham, UK"}]},{"given":"Ricardo J.","family":"Camacho","sequence":"additional","affiliation":[{"name":"Centro de Mal\u00e1ria e outras Doen\u00e7as Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal"},{"name":"Laborat\u00f3rio de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal"}]},{"given":"Vincent","family":"Soriano","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain"}]},{"given":"Patrick","family":"Goubau","sequence":"additional","affiliation":[{"name":"AIDS Reference Laboratory, Universit\u00e9 Catholique de Louvain, Brussels, Belgium"}]},{"given":"Jo\u00e3o D.","family":"de Sousa","sequence":"additional","affiliation":[{"name":"Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium"}]},{"given":"Anne-Mieke","family":"Vandamme","sequence":"additional","affiliation":[{"name":"Centro de Mal\u00e1ria e outras Doen\u00e7as Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal"},{"name":"Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium"}]},{"given":"Marc A.","family":"Suchard","sequence":"additional","affiliation":[{"name":"Departments of Biomathematics and Human Genetics, David Geffen School of Medicine; Department of Biostatistics, School of Public Health; University of California, Los Angeles, USA"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium"}]}],"member":"345","reference":[{"key":"r1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM198905253202119"},{"key":"r2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki063"},{"key":"r3","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr481"},{"key":"r4","doi-asserted-by":"publisher","DOI":"10.1089\/088922203322230905"},{"key":"r5","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1997.13.401"},{"key":"r6","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(87)90043-2"},{"key":"r7","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1128\/JVI.70.6.3617-3627.1996","article-title":"Genetic characterization of new West African simian immunodeficiency virus SIVsm: geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty mangabey troop","volume":"70","author":"Chen","year":"1996","journal-title":"J Virol"},{"key":"r8","doi-asserted-by":"crossref","first-page":"3953","DOI":"10.1128\/JVI.71.5.3953-3960.1997","article-title":"Human immunodeficiency virus type 2 (HIV-2) seroprevalence and characterization of a distinct HIV-2 genetic subtype from the natural range of simian immunodeficiency virus-infected sooty mangabeys","volume":"71","author":"Chen","year":"1997","journal-title":"J Virol"},{"key":"r9","doi-asserted-by":"publisher","DOI":"10.1089\/apc.2007.0149"},{"key":"r10","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e328300a33d"},{"key":"r11","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2000.0685"},{"key":"r12","doi-asserted-by":"publisher","DOI":"10.1089\/0889222041217392"},{"key":"r13","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199005000-00010"},{"key":"r14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009936"},{"key":"r15","first-page":"358","article-title":"The epidemic of HIV\/AIDS in Abidjan, C\u00f4te d\u2019Ivoire: a review of data collected by Project RETRO-CI from 1987 to 1993","volume":"10","author":"Djomand","year":"1995","journal-title":"J Acquir Immune Defic Syndr Hum Retrovirol"},{"key":"r16","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-7-214"},{"key":"r17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0040088"},{"key":"r18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2011.05.058"},{"key":"r19","doi-asserted-by":"publisher","DOI":"10.1097\/00042560-199711010-00010"},{"key":"r20","doi-asserted-by":"publisher","DOI":"10.1038\/358495a0"},{"key":"r21","author":"Garcia","year":"2000","journal-title":"Portugal Migrante \u2013 Emigrantes e Imigrados, dois estudos introdut\u00f3rios"},{"key":"r22","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(03)00797-7"},{"key":"r23","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1128\/JVI.68.4.2161-2168.1994","article-title":"Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses","volume":"68","author":"Grez","year":"1994","journal-title":"J Virol"},{"key":"r24","doi-asserted-by":"publisher","DOI":"10.1126\/science.287.5453.607"},{"key":"r25","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.62.081307.162912"},{"key":"r26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki198"},{"key":"r27","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(89)91760-1"},{"key":"r28","doi-asserted-by":"publisher","DOI":"10.1126\/science.1126531"},{"key":"r29","doi-asserted-by":"publisher","DOI":"10.3109\/00365549209052626"},{"key":"r30","first-page":"16","article-title":"HIV-1\/2 seroprevalence in Guinea Conakry","volume":"6","author":"Lakiss","journal-title":"VII International Conference on AIDs"},{"key":"r31","doi-asserted-by":"publisher","DOI":"10.1016\/0035-9203(89)90350-7"},{"key":"r32","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.3201\/eid1310.070338","article-title":"Exposure to wild primates among HIV-infected persons","volume":"13","author":"LeBreton","year":"2007","journal-title":"Emerg Infect Dis"},{"key":"r33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0936469100"},{"key":"r34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000520"},{"key":"r35","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.296.6615.83"},{"key":"r36","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e32832cedfb"},{"key":"r37","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2001.0867"},{"key":"r38","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn090"},{"key":"r39","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.44.4.1543-1546.2006"},{"key":"r40","first-page":"125","article-title":"Laboratory diagnosis of the first cases of HIV-2 infection in Canada","volume":"140","author":"Neumann","year":"1989","journal-title":"CMAJ"},{"key":"r41","doi-asserted-by":"publisher","DOI":"10.1038\/332295d0"},{"key":"r42","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2008.04059.x"},{"key":"r43","year":"2011"},{"key":"r44","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-6-49"},{"key":"r45","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2007.08.001"},{"key":"r46","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1998.14.51"},{"key":"r47","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000232239.05545.33"},{"key":"r48","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199111000-00002"},{"key":"r49","doi-asserted-by":"publisher","DOI":"10.1089\/088922299311132"},{"key":"r50","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199006283222614"},{"key":"r51","doi-asserted-by":"publisher","DOI":"10.1086\/315010"},{"key":"r52","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn083"},{"key":"r53","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(89)92281-2"},{"key":"r54","first-page":"941","article-title":"HIV-2 infection in Bissau, West Africa, 1987-1989: incidence, prevalences, and routes of transmission","volume":"6","author":"Poulsen","year":"1993","journal-title":"J Acquir Immune Defic Syndr"},{"key":"r55","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(96)04402-9"},{"key":"r56","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2583"},{"key":"r57","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.4.395"},{"key":"r58","author":"Rambaut","year":"2007"},{"key":"r59","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199407000-00016"},{"key":"r60","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2007.0034"},{"key":"r61","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.19.12515-12527.2005"},{"key":"r62","doi-asserted-by":"publisher","DOI":"10.1093\/ije\/20.2.480"},{"key":"r63","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-5-103"},{"key":"r64","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01921-10"},{"key":"r65","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-9071(200005)61:1<111::AID-JMV18>3.0.CO;2-W"},{"key":"r66","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp244"},{"key":"r67","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1093\/oxfordjournals.molbev.a003872","article-title":"Bayesian selection of continuous-time Markov chain evolutionary models","volume":"18","author":"Suchard","year":"2001","journal-title":"Mol Biol Evol"},{"key":"r68","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1997.13.621"},{"key":"r69","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkr164"},{"key":"r70","first-page":"1","article-title":"AIDS epidemic update 2006","year":"2006"},{"key":"r71","year":"2010"},{"key":"r72","doi-asserted-by":"publisher","DOI":"10.1086\/597504"},{"key":"r73","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1097\/QAI.0b013e3181bf1a25","article-title":"Two distinct epidemics: the rise of HIV-1 and decline of HIV-2 infection between 1990 and 2007 in rural Guinea-Bissau","volume":"53","author":"van Tienen","year":"2009","journal-title":"J Acquir Immune Defic Syndr"},{"key":"r74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000377"},{"key":"r75","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199112000-00018"},{"key":"r76","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.3201\/eid1112.040789","article-title":"Bushmeat hunting, deforestation, and prediction of zoonoses emergence","volume":"11","author":"Wolfe","year":"2005","journal-title":"Emerg Infect Dis"},{"key":"r77","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2005.21.17"}],"container-title":["Journal of General Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.038638-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,26]],"date-time":"2020-10-26T23:32:40Z","timestamp":1603755160000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.038638-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4,1]]},"references-count":77,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2012,4,1]]}},"URL":"https:\/\/doi.org\/10.1099\/vir.0.038638-0","relation":{},"ISSN":["0022-1317","1465-2099"],"issn-type":[{"value":"0022-1317","type":"print"},{"value":"1465-2099","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,4,1]]}}}