Population dynamics of HIV-1 inferred from gene sequences

A method for the estimation of population dynamic history from sequence dat a is described and used to investigate the past population dynamics of HIV- 1 subtypes A and B. Using both gag and env gene alignments the effective po pulation size of each subtype is estimated and found to be surprisingly sma ll. This may be a result of the selective sweep of mutations through the po pulation, or may indicate an important role of genetic drift in the fixatio n of mutations. The implications of these results for the spread of drug-re sistant mutations and transmission dynamics, and also the roles of selectio n and recombination in shaping HIV-1 genetic diversity, are discussed. A la rger estimated effective population size for subtype A may be the result of differences in time of origin, transmission dynamics, and/or population st ructure. To investigate the importance of population structure a model of p opulation subdivision was fitted to each subtype, although the improvement in likelihood was found to be nonsignificant.