Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data

摘要: The within-host evolution of influenza is a vital component its epidemiology. A question particular interest the role that selection plays in shaping viral population over course single infection. We here describe method to measure acting upon virus within an individual host, based time-resolved genome sequence data from Analysing transmission study conducted pigs, describing part haemagglutinin gene (HA1) virus, we find signatures non-neutrality six total sixteen infections. evidence for both positive and negative specific alleles, while three cases, suggest presence time-dependent selection. In one infection observe what potentially immune response against virus; non-synonymous mutation epitope region found be under initially positive, then strongly Crucially, given lack homologous recombination influenza, our accounts linkage disequilibrium between nucleotides at different positions gene, allowing analysis populations which multiple mutations are present any time. Our approach offers new insight into dynamics infection, providing detailed characterisation forces underlie evolution.