Abstract

PIP: HIV-1 is spreading at an exponential rate in southern Africa, with a current doubling time of approximately one year. An estimated 2 million of South Africa's 36 million population are already infected with HIV. Information on the extent of variability of HIV-1 sequences in the region is important for the development of vaccines, the evaluation of new therapies, and for structure/function studies of the viral genome and proteins. The authors isolated and partially sequenced local strains of the virus. The first strain sequenced was determined to be a new subtype of HIV-1, designated subtype C(2). HIV-1 subtypes B and D are also circulating within southern Africa. The derived phylogenetic trees for the various strains are presented. It is possible that southern African HIV-1 strains have evolved from Central African ones during their spread southward over time and geographic distance. The data on HIV-1 env and gag gene variability presented in this paper have implications for the design of vaccines intended for use in southern Africa and India. The results also establish new limits of variability for the virus, by extending the phylogenetic tree along a new branch.