Abstract:
Background: HIV-1 molecular epidemiology amongst men who have sex with men
(MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine
HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR)
in acute and early infected MSM from Coastal Kenya.
Methods: Analysis of HIV-1 partial pol sequences from MSM recruited 2005-2017 and
sampled within six months of the estimated date of infection. Volunteers were classified
as men who have sex with men exclusively (MSME) or with both men and women
(MSMW). HIV-1 subtype and transmission clusters were determined by maximumlikelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug
resistance database.
Results: Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had
HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters,
with substantial mixing between MSME and MSMW. Majority of volunteer sequences
were either not linked to any reference sequence (56%) or clustered exclusively with
sequences of Kenyan origin (19%). Eight (8% [95% CI: 4-16]) had at least one TDR
mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse
transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with
sequences forming transmission clusters of two and three taxa each. There were no
significant differences in HIV-1 subtype distribution and TDR between MSME and
MSMW.
Conclusions: This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan
origin, with many transmission clusters and having intermediate level of TDR. Targeted
HIV-1 prevention, early identification and care interventions are warranted to break the
transmission cycle amongst MSM from Coastal Kenya.