Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda

The molecular epidemiology of a population-based cohort in a cluster of 15 villages in southwestern Uganda was investigated by sequencing part of the p24 gag gene and performing heteroduplex mobility assays (HMAs) of the V3 r egion of the env gene. Sequence and HMA data, obtained for 69 and 88 provir uses, respectively, showed that the clade A and D viruses were present at a ratio of about 0.67:1. No other clades mere detected. Thirteen (22%) of 59 proviruses for which both gag and env data were obtained appeared to be re combinants, Although both clade A and D viruses were present in 13 of the v illages, their distribution was unequal: for example, from env data 59% of clade A viruses were found in the eastern villages, compared with only 27% of clade D viruses, Phylogenetic (maximum likelihood) analysis of the p24 g ag sequences showed a total of five clusters supported by bootstrap resampl ing values above or close to 75%. Four clusters were sexual partners, but t here was no known sexual contact between the persons in the other cluster. The DNA sequences showed between 0.5 and 8.3% divergence from the cohort cl ade A or D consensus sequences. The sequences were not closely related to t hose published for other clade A or D proviruses.