Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Autoři: Nuno R. Faria aff001;  Nicole Vidal aff002;  José Lourenco aff001;  Jayna Raghwani aff001;  Kim C. E. Sigaloff aff003;  Andy J. Tatem aff005;  David A. M. van de Vijver aff007;  Andrea-Clemencia Pineda-Peña aff008;  Rebecca Rose aff010;  Carole L. Wallis aff011;  Steve Ahuka-Mundeke aff012;  Jean-Jacques Muyembe-Tamfum aff012;  Jérémie Muwonga aff013;  Marc A. Suchard aff014;  Tobias F. Rinke de Wit aff003;  Raph L. Hamers aff003;  Nicaise Ndembi aff015;  Guy Baele aff016;  Martine Peeters aff002;  Oliver G. Pybus aff001;  Philippe Lemey aff016;  Simon Dellicour aff016
Působiště autorů: Department of Zoology, University of Oxford, Oxford, United Kingdom aff001;  TransVIHMI, Institut de Recherche pour le Développement, INSERM, and University of Montpellier, Montpellier, France aff002;  Amsterdam Institute for Global Health and Development, Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands aff003;  Department of Internal Medicine, Section of Infectious Diseases, VU University Medical Center, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands aff004;  Department of Geography and Environment, University of Southampton, Southampton, United Kingdom aff005;  Flowminder Foundation, Stockholm, Sweden aff006;  Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands aff007;  Global Health and Tropical Medicine—Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal aff008;  Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia aff009;  Bioinfoexperts, LLC, Thibodaux, Los Angeles, United States of America aff010;  Department of Molecular Pathology, Lancet Laboratories and BARC-SA, Johannesburg, South Africa aff011;  Institut National de Recherche Biomedicales, Kinshasa, Democratic Republic of Congo and Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo aff012;  AIDS national laboratory and Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo aff013;  Departments of Biomathematics and Human Genetics David Geffen School of Medicine at UCLA, and Department of Biostatistics UCLA School of Public Health, Los Angeles, United States of America aff014;  Institute of Human Virology, Abuja, Nigeria aff015;  KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium aff016;  Spatial Epidemiology Lab, Université Libre de Bruxelles, Bruxels, Belgium aff017
Vyšlo v časopise: Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 15(12): e32767. doi:10.1371/journal.ppat.1007976
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1007976


Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.

Klíčová slova:

Africa – HIV epidemiology – HIV-1 – Phylogenetic analysis – Phylogenetics – Phylogeography – Sequence analysis – Uganda


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