Background:  As part of an investigation of increased HIV diagnoses among young (16 to 25 years-old), black men who have sex with men (MSM) in Mississippi, we evaluated phylogenetic clustering of HIV-1 protease-reverse transcriptase sequences from persons living in Mississippi and described those clusters that included young black MSM.

Methods:  We analyzed viral sequences from 797 drug-naive persons (including 130 young black MSM), who were newly diagnosed with HIV in Mississippi during 2005 to 2008, using neighbor-joining, maximum likelihood, and Bayesian inference. A stringent cutoff of ≥99% bootstrap support and nucleotide identity was used to define phylogenetic clusters. We used surveillance data to examine demographic attributes and risk factors of all persons in clusters that included young black MSM. Furthermore, we used data obtained through interviews with 26 young black MSM to compare behavioral characteristics of those in clusters with those who are not in clusters. Major mutations conferring drug resistance were defined according to the December 2008 International AIDS Society-USA guidelines.

Results:  Eighty-three phylogenetic clusters were identified, 22 (24%) of which included HIV strains from young black MSM. Of the 69 persons in these clusters, all were male, 66 (96%) were black, 61 (88%) were MSM (the rest were unknown), 55 (80%) were 16 to 25 years old, and 20 (29%) had transmitted drug resistance. Among the 26 interviewed young black MSM, HIV strains from 13 (50%) were involved in 10 clusters. Of the 40 persons in these clusters, all were men, 38 (95%) were black, 37 (93%) were MSM (the rest were unknown), 32 (80%) were 16 to 25 years old, and 16 (40%) had transmitted drug resistance. The 13 interviewed cases who were in clusters were more likely to report illicit drug use (62% vs 23%, P =0.05) or exchange sex (31% vs 0%, P =0.03) than the 13 non-clustered interviewed cases.

Conclusions:  Phylogenetic analysis identified clusters involving HIV-infected young black MSM in Mississippi. The homogeneity of these clusters with respect to sex, race, transmission category, and age suggests insularity of this population with respect to HIV transmission. Reducing HIV transmission among young black MSM in Mississippi may require prevention strategies that are tailored to young black MSM and those in their sexual networks. Investigating sources and interrupting transmission in this group is particularly important given the high proportion with transmitted drug resistance.