Viral host shifts

Abstract

Newly emerging infectious diseases present some of the most pressing challenges facing human health, wildlife conservation and veterinary medicine. A disproportionate number of emerging pathogens are RNA viruses that originate in other species through a process termed ‘cross-species transmission.’ Mechanisms underlying viral emergence in new species remain poorly understood, despite the importance of emergence events for human and wildlife health. This dissertation explores the ecological and evolutionary factors that contribute to the emergence of rabies virus in new host species using bats as a model system. By constructing large datasets of viral sequences from North and South American bat species, I first examined the effects of host ecology and phylogeny on rates of cross-species transmission and viral evolution. Next, I combined evolutionary and demographic inference to demonstrate links between the extent of adaptive evolution associated with the establishment of rabies virus in new bat species and the speed of emergence in new bat species. Through a field study, I examined the transmission dynamics of rabies within populations of a single species, common vampire bats, to enhance prospects for rabies prevention in humans and domesticated animals. Together, these findings develop a framework for dissecting viral host shifts into quantifiable sequential processes and constitute a step towards the ultimate goal of predicting which host shifts are most likely to occur and what measures can be taken to prevent them.