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Abstract
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 ‘hotspots’ 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 per cent of the epidemic in Kenya) sampled 1986–2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per 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.
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1 Department of Translational Medicine, Lund University , Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
2 Nyanza Reproductive Health Society , United Mall, P.O. Box 1764, Kisumu, Kenya
3 Department of Medical Microbiology, University of Nairobi , P.O. Box 30197-00100, Nairobi, Kenya
4 Kenya Medical Research Institute-Wellcome Trust Research Programme , KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
5 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
6 Kenya Medical Research Institute/Center for Global Health Research , KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
7 Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi , P.O. Box 19676-00202, Nairobi, Kenya
8 IAVI Global Headquarters , 125 Broad Street, 9th Floor, New York, NY 10004, USA
9 Nuffield Department of Medicine, The University of Oxford , Old Road Campus, Headington, Oxford OX3 7BN, UK
10 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