title: Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.
abstract: 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 pol and 248 partial env 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 Côte d'Ivoire 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, Côte d'Ivoire 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.
authors.affiliation: Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
authors.forename: Nuno R
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Hodges-Mameletzis
authors.affiliation: Laboratório de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal.
authors.forename: Joana C
authors.initials: JC
authors.lastname: Silva
authors.affiliation: Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
authors.forename: Berta
authors.initials: B
authors.lastname: Rodés
authors.affiliation: HPA Birmingham, Heartlands Hospital, Birmingham, UK.
authors.forename: Smit
authors.initials: S
authors.lastname: Erasmus
authors.affiliation: Fondazione IRCCS Policlinico, San Matteo, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Paolucci
authors.affiliation: AIDS Reference Laboratory, Université Catholique de Louvain, Brussels, Belgium.
authors.forename: Jean
authors.initials: J
authors.lastname: Ruelle
authors.affiliation: Incidence and Case Surveillance Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Danuta
authors.initials: D
authors.lastname: Pieniazek
authors.affiliation: Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisboa, Portugal.|Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.|Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Taveira
authors.affiliation: Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Treviño
authors.affiliation: Laboratório de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal.
authors.forename: Maria F
authors.initials: MF
authors.lastname: Gonçalves
authors.affiliation: Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
authors.forename: Sabelle
authors.initials: S
authors.lastname: Jallow
authors.affiliation: HPA Birmingham, Heartlands Hospital, Birmingham, UK.
authors.forename: Li
authors.initials: L
authors.lastname: Xu
authors.affiliation: Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.|Laboratório de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal.
authors.forename: Ricardo J
authors.initials: RJ
authors.lastname: Camacho
authors.affiliation: Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
authors.forename: Vincent
authors.initials: V
authors.lastname: Soriano
authors.affiliation: AIDS Reference Laboratory, Université Catholique de Louvain, Brussels, Belgium.
authors.forename: Patrick
authors.initials: P
authors.lastname: Goubau
authors.affiliation: Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
authors.forename: João D
authors.initials: JD
authors.lastname: de Sousa
authors.affiliation: Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.|Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
authors.forename: Anne-Mieke
authors.initials: AM
authors.lastname: Vandamme
authors.affiliation: Departments of Biomathematics and Human Genetics, David Geffen School of Medicine; Department of Biostatistics, School of Public Health; University of California, Los Angeles, USA.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.affiliation: Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
mesh_terms: D000354:Africa, Western; D001499:Bayes Theorem; D055726:Cabo Verde; D018595:Colonialism / Q000266:history; D007560:Cote d'Ivoire; D005814:Genes, Viral / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D006169:Guinea-Bissau; D015658:HIV Infections / Q000266:history* / Q000821:virology; D015498:HIV-2 / Q000235:genetics*; D049673:History, 20th Century; D006801:Humans; D008969:Molecular Sequence Data; D058974:Phylogeography; D012675:Senegal