Our objective was to monitor changes in the subtypes of HIV-1 infecting a rural Ugandan cohort where the spread of HIV-1 is by unprotected heterosexual contact and subtypes A and D predominate. Should one subtype be better able to spread we would anticipate a rise in incidence of one subtype at the expense of the other over a decade of study. We employed a natural history cohort, which had been established by the Medical Research Council in 1990 and subtyped virus from 90% (139) incident cases by DNA sequencing in two separate genes. We found that viral subtype had no predilection for males, females or age at infection and that between 1990 and 2000 there was no significant change in the relative number of different subtypes. The only significant trend was a reduction in the proportion of viruses classified as recombinant. This may reflect the overall decline in prevalence of HIV-1 in Uganda over this period.
