Host constraints on viral recombination and emergence

Recombination (including reassortment) is a salient force in viral evolution, which has been implicated in the emergence of several zoonotic pathogens in human populations. Viral recombination occurs during simultaneous infection of an individual host with multiple strains (co-infection). This means that processes which affect the incidence of a disease in the host population affect how often viral genotypes recombine. We investigate whether and how host traits influence the rate of viral recombination using a mathematical model that makes feedbacks between viral evolution and host ecology explicit. Using approximations from population genetics, we find that viruses of host species that are short-lived, acutely infected, or whose immunity wanes quickly recombine more frequently than those of hosts that are relatively long-lived, chronically infected, and have long-lasting immunity. This is because of differences in the density of (co-)infections at equilibrium. Using highly pathogenic avian influenza sequence data we test the prediction that recombination is elevated in short-lived hosts. In agreement with this prediction, the magnitude of statistical associations between mutations on different segments of the flu genome increases with host body size, a proxy for lifespan. We discuss the implications of these findings for emergence.