A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory.

ABSTRACT: Fitness is a central quantity in evolutionary models of viruses. However, it remains difficult to determine viral fitness experimentally, and existing in vitro assays can be poor predictors of in vivo fitness of viral populations within their hosts. Next-generation sequencing can nowadays provide snapshots of evolving virus populations, and these data offer new opportunities for inferring viral fitness. Using the equilibrium distribution of the quasispecies model, an established model of intrahost viral evolution, we linked fitness parameters to the composition of the virus population, which can be estimated by next-generation sequencing. For inference, we developed a Bayesian Markov chain Monte Carlo method to sample from the posterior distribution of fitness values. The sampler can overc

SUBMITTER: Seifert D 

PROVIDER: S-EPMC4286684 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature