{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T12:57:13Z","timestamp":1783515433950,"version":"3.55.0"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,3,3]],"date-time":"2022-03-03T00:00:00Z","timestamp":1646265600000},"content-version":"vor","delay-in-days":61,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Interne Fondsen KU Leuven","award":["C14\/18\/094"],"award-info":[{"award-number":["C14\/18\/094"]}]},{"name":"Sub-Saharan African Network for TB\/HIV Research Excellence","award":["DEL-15-006"],"award-info":[{"award-number":["DEL-15-006"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["725422-ReservoirDOCS"],"award-info":[{"award-number":["725422-ReservoirDOCS"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fonds voor Wetenschappelijk Onderzoek - Vlaanderen","award":["G066215N, G0D5117N, G0B9317N, and G0E1420N"],"award-info":[{"award-number":["G066215N, G0D5117N, G0B9317N, and G0E1420N"]}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2016-01417"],"award-info":[{"award-number":["2016-01417"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 \u2018hotspots\u2019 and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3\u2009per cent of the epidemic in Kenya) sampled 1986\u20132019 from individuals of different risk groups and regions in Kenya. We found 89\u2009per cent within-risk group transmission and 11\u2009per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.<\/jats:p>","DOI":"10.1093\/ve\/veac016","type":"journal-article","created":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T12:11:14Z","timestamp":1646136674000},"source":"Crossref","is-referenced-by-count":18,"title":["Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study"],"prefix":"10.1093","volume":"8","author":[{"given":"George M","family":"Nduva","sequence":"first","affiliation":[{"name":"Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden"},{"name":"Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederick","family":"Otieno","sequence":"additional","affiliation":[{"name":"Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Kimani","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Wahome","sequence":"additional","affiliation":[{"name":"Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lyle R","family":"McKinnon","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada"},{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francois","family":"Cholette","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada"},{"name":"National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell","family":"Majiwa","sequence":"additional","affiliation":[{"name":"Kenya Medical Research Institute\/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moses","family":"Masika","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaudensia","family":"Mutua","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omu","family":"Anzala","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan M","family":"Graham","sequence":"additional","affiliation":[{"name":"Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya"},{"name":"Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larry","family":"Gelmon","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya"},{"name":"Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt A","family":"Price","sequence":"additional","affiliation":[{"name":"IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA"},{"name":"Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian D","family":"Smith","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert C","family":"Bailey","sequence":"additional","affiliation":[{"name":"Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya"},{"name":"Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1915-7732","authenticated-orcid":false,"given":"Guy","family":"Baele","sequence":"additional","affiliation":[{"name":"KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amin S","family":"Hassan","sequence":"additional","affiliation":[{"name":"Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden"},{"name":"Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduard J","family":"Sanders","sequence":"additional","affiliation":[{"name":"Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya"},{"name":"Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joakim","family":"Esbj\u00f6rnsson","sequence":"additional","affiliation":[{"name":"Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden"},{"name":"Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,3,3]]},"reference":[{"key":"2022032913095553200_R1","doi-asserted-by":"crossref","DOI":"10.1097\/COH.0000000000000542","article-title":"PANGEA-HIV 2: Phylogenetics and Networks for Generalised Epidemics in Africa","volume":"14","author":"Abeler-D\u00f6rner","year":"2019","journal-title":"Current Opinion in HIV and 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