A framework including recombination for analyzing the dynamics of within-host HIV genetic diversity.

ABSTRACT: This paper presents a novel population genetic model and a computationally and statistically tractable framework for analyzing within-host HIV diversity based on serial samples of HIV DNA sequences. This model considers within-host HIV evolution during the chronic phase of infection and assumes that the HIV population is homogeneous at the beginning, corresponding to the time of seroconversion, and evolves according to the Wright-Fisher reproduction model with recombination and variable mutation rate across nucleotide sites. In addition, the population size and generation time vary over time as piecewise constant functions of time. Under this model I approximate the genealogical and mutational processes for serial samples of DNA sequences by a continuous coalescent-recombination process an

SUBMITTER: Sargsyan O 

PROVIDER: S-EPMC3917834 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature