Ecological and evolutionary dynamics of multi-strain RNA viruses

Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host–pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses. Many viruses evolve quickly, leading to the coexistence of multiple strains within the same host and population. In this Review, the authors synthesize ecological and evolutionary approaches to studying the dynamics of multi-strain RNA virus infections and suggest opportunities for future work.