Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection.

ABSTRACT: Analysis of HIV-1 gene sequences sampled longitudinally from infected individuals can reveal the evolutionary dynamics that underlie associations between disease outcome and viral genetic diversity and divergence. Here we extend a statistical framework to estimate rates of viral molecular adaptation by considering sampling error when computing nucleotide site-frequencies. This is particularly beneficial when analyzing viral sequences from within-host viral infections if the number of sequences per time point is limited. To demonstrate the utility of this approach, we apply our method to a cohort of 24 patients infected with HIV-1 at birth. Our approach finds that viral adaptation arising from recurrent positive natural selection is associated with the rate of HIV-1 disease progression, in

SUBMITTER: Raghwani J 

PROVIDER: S-EPMC4704780 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature