title: HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.
abstract: Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
authors.forename: Nuno R
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095-1766, USA. Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095-1766, USA.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Baele
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Ward
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Tatem
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium. Centro de Malária e outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal.
authors.forename: João D
authors.initials: JD
authors.lastname: Sousa
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Nimalan
authors.initials: N
authors.lastname: Arinaminpathy
authors.affiliation: Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CHUS, 3001, 12ème Avenue Nord, Sherbrooke, QC J1H 5N4, Canada.
authors.forename: Jacques
authors.initials: J
authors.lastname: Pépin
authors.affiliation: Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Posada
authors.affiliation: Laboratoire Retrovirus, UMI233, Institut de Recherche pour le Développement and University of Montpellier, 911 Avenue Agropolis, BP5045, 34032 Montpellier, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Peeters
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. philippe.lemey@rega.kuleuven.be oliver.pybus@zoo.ox.ac.uk.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium. philippe.lemey@rega.kuleuven.be oliver.pybus@zoo.ox.ac.uk.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology* / Q000266:history / Q000635:transmission; D021821:Communicable Diseases, Emerging / Q000453:epidemiology* / Q000266:history / Q000635:transmission; D015023:Democratic Republic of the Congo; D019143:Evolution, Molecular; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000502:physiology*; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D058873:Pandemics / Q000266:history; D010802:Phylogeny; D011157:Population Dynamics / Q000266:history; D011995:Recombination, Genetic; D014507:Urbanization / Q000266:history / Q000639:trends