Reservoir population dynamics and pathogen epidemiology drive pathogen genetic diversity, spillover, and emergence

When several factors align, pathogens that normally infect wildlife can spill over into the human population. If pathogen transmission within the human population is self-sustaining, or rapidly evolves to be self sustaining, novel human pathogens can emerge. Although many factors influence the likelihood of spillover and emergence, the rate of contact between humans and wildlife is critical. Thus, for those pathogens inhabiting wildlife reservoirs with pronounced seasonal fluctuations in population density, it is broadly recognized that spillover risk also varies with season. What remains unknown, however, is the extent to which seasonal fluctuations in reservoir populations influence the evolutionary dynamics of pathogens in ways that affect the likelihood of emergence. Here, we use mathematical models and stochastic simulations to show that seasonal fluctuations in reservoir population densities lead to seasonal increases in genetic variation within pathogen populations and thus influence the waiting time for mutations capable of sustained human-to-human transmission. These seasonal increases in genetic variation also lead to elevated risk of emergence at predictable times of year.