Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

ABSTRACT: A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within and among its various subtypes. Two complementary hypotheses are suggested to explain the sequence variability among HIV-1 subtypes. The first suggests that the functional constraints at each site remain the same across all subtypes, and the differences among subtypes are a direct reflection of random substitutions, which have occurred during the time elapsed since their divergence. The alternative hypothesis suggests that the functional constraints themselves have evolved, and thus sequence differences among subtypes in some sites reflect shifts in function. To determine the contribution of each of these two alternatives to HIV-1 subtype evolution, we have developed a novel Bayesian method for t

SUBMITTER: Penn O 

PROVIDER: S-EPMC2566816 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature