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We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men MSM and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, other men, and women from to Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. S ex between men has only recently been recognized as an important route of HIV-1 transmission in sub-Saharan Africa. Several molecular phylogenetic studies have shown the potential of HIV-1 polymerase pol sequences to provide insight into HIV-1 transmission networks, revealing infections related by time, geographic area, and risk group. Sequences were selected from a cohort study among MSM and female sex workers FSW in coastal Kenya and MSM sex workers in Nairobi, and from female and male patients who participated in antiretroviral drug resistance monitoring studies in hospital-based clinics in the same geographic areas.

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