On a Neutral Host-Virus Model with Recombination

Abstract: Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus particles replicate, recombine, and mutate within their hosts at rates that act on different time scales. Furthermore, virus particles are exchanged between hosts at reinfection events and hosts are replaced by primary infected hosts when they die. We determine the asymptotic type distribution observed in a single host in the limit of large host and virus populations under asymptotic rate assumptions by tracing back the ancestry of the sample. The proposed model may serve as a null model for the evolution of virus populations that are capable of persistence and can be used to estimate the strengths of different evolutionary forces driving genetic diversity, see also [4].