Genetic analysis of the complete gag and env genes of HIV type 1 subtype Cprimary isolates from South Africa

South Africa has one of the fastest growing HIV-1 epidemics, with an estima ted 4.7 million people infected. To better understand the genetic diversity of this epidemic and its potential impact on vaccine development, we have cloned and sequenced the complete gag and env genes of 13 primary virus iso lates. Phylogenetic analysis of our sequences and 69 complete env genes fro m the Los Alamos and GenBank databases revealed multiple subclusters within subtype C. The V3 loop region was relatively conserved in all our strains when compared with other subtypes, but the region immediately downstream wa s highly variable. No intersubtype recombinant forms were observed when com paring the gag and env sequences. Characterization of the complete gag and env genes enabled us to select specific strains for further vaccine develop ment.