Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006–2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2–20 sequences) were found—half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017–2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
Highlights
In sub-Saharan Africa, the HIV-1 epidemic among men who have sex with men (MSM) has only recently received attention—and the role of MSM in HIV-1 transmission has been acknowledged (Beyrer et al, 2010; Sanders et al, 2015a; Nduva et al, 2021)
New sequences were generated from blood plasma obtained through studies conducted through the MSM Health Research Consortium—a multisite collaboration between researchers affiliated with Kenya Medical Research Institute (KEMRI)-Wellcome Trust (KWTRP) in Coastal Kenya, Nyanza Reproductive Health Society (NRHS) in Nyanza, and Sex Workers Outreach Program (SWOP) clinics in Nairobi
NonKenyan HIV-1 reference sequences were obtained from GenBank based on similarity
Summary
In sub-Saharan Africa, the HIV-1 epidemic among men who have sex with men (MSM) has only recently received attention—and the role of MSM in HIV-1 transmission has been acknowledged (Beyrer et al, 2010; Sanders et al, 2015a; Nduva et al, 2021). There is evidence of high mobility of MSM sex workers between regions, which could link HIV-1 transmissions in different regions (Geibel et al, 2008). The Ministry of Health in Kenya through the National AIDS Control Council (NACC) has made efforts to strengthen HIV healthcare services for MSM (Gruskin and Tarantola, 2008; van der Elst et al, 2020). Geographic mobility has been shown to play an important role in HIV-1 dispersal (Faria et al, 2014; Grabowski et al, 2020). It is possible that spatial differences in the HIV1 distribution in Kenya combined with geographically mobile MSM sex workers could impact HIV-1 spread among MSM throughout the country (Faria et al, 2014; Grabowski et al, 2020). Clear data on HIV-1 transmission dynamics within and between MSM in different geographic regions are lacking in Kenya
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