To better characterize the virus isolates associated with the HIV-1 epidemi
c in Uganda, 100 specimens from HIV-1-infected persons were randomly select
ed from each of two periods from late 1994 to late 1997. The 200 specimens
were classified into HIV-1 subtypes by sequence-based phylogenetic analysis
of the envelope (env) gp41 region; 98 (49%) were classified as env subtype
A, 96 (48%) as D, 5 (2.5%) as C, and 1 was not classified as a known env s
ubtype. Demographic characteristics of persons infected with the two princi
pal HIV-1 subtypes, A and D, were Very similar, and the proportion of eithe
r subtype did not differ significantly between early and later periods. Our
systematic characterization of the HIV-1 epidemic in Uganda over an almost
3-year period documented that the distribution and degree of genetic diver
sity of the HIV subtypes A and D are very similar and did not change apprec
iably over that time.