A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.

ABSTRACT: In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from

SUBMITTER: Illingworth CJR 

PROVIDER: S-EPMC7295245 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature