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, 226 other
men, and 364 women from 2005 to 2010. 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. Finally, we compared
84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences
from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both
locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant
HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype
A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank
comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of
MSM and heterosexual HIV-1 epidemics in Kenya.