Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.

ABSTRACT: Human immunodeficiency virus (HIV) is a rapidly evolving pathogen that causes chronic infections, so genetic diversity within a single infection can be very high. High-throughput "deep" sequencing can now measure this diversity in unprecedented detail, particularly since it can be performed at different time points during an infection, and this offers a potentially powerful way to infer the evolutionary dynamics of the intrahost viral population. However, population genomic inference from HIV sequence data is challenging because of high rates of mutation and recombination, rapid demographic changes, and ongoing selective pressures. In this article we develop a new method for inference using HIV deep sequencing data, using an approach based on importance sampling of ancestral recombination

SUBMITTER: Dialdestoro K 

PROVIDER: S-EPMC4905535 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature