Background: We investigated the evolutionary and biogeographic history of HIV-1 subtype C, as revealed by the diversity of DNA sequences, using computational methods refined by Korber et al.
Methods: Using maximum likelihood code modified for use on a massively parallel supercomputer, we performed phylogenetic analyses of 2 new data sets of DNA sequences. These data sets consist of 100 complete genomes (10,000 bases) and 180 env genes (2,800 bases).
Results: We located the phylogenetic root node of the subtype C clade and estimated its age. We examined subtype C sequences from India and related sequences from China to test the hypothesis that there are 2 separate vectors for transmission of HIV in India. Similarly, we identified major phylogenetic clades within subtype C in Africa.
Conclusions: As the volume of HIV sequence data increases, phylogenetic analyses reveal consistent patterns in the subtype C clade. These patterns may be relevant to the design of vaccines and vaccination programs. Conversely, phylogenetic analyses of large quantities of data also reveal specific areas within the subtype C clade that as yet do not show consistent patterns. To resolve these problem areas, new data are needed, particularly longer DNA sequences from samples that have early collection dates. Early samples represented in the HIV genome database at LANL are ideal candidates for further sequencing.