Making sense of the virome in light of evolution and ecology

Understanding the patterns and drivers of viral prevalence is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these ‘virome’ studies are primarily descriptive, our understanding of the predictors of virus prevalence and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g., seasonality, habitat) versus evolutionary predictors (e.g., host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to determine what factors predict the composition of the virome of individual hosts, populations, or species. In addition, most studies of virus ecology represent a snapshot of single viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesising evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for further work to quantify the drivers of virus prevalence and diversity.