Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential

The high replication and mutation rates of RNA viruses can result in the emergence of new epidemic variants. Thus, the ability to follow host-specific evolutionary trajectories of viruses is essential to predict and prevent epidemics. By studying the spatial and temporal evolution of chikungunya virus during natural transmission between mosquitoes and mammals, we have identified viral evolutionary intermediates prior to emergence. Analysis of virus populations at anatomical barriers revealed that the mosquito midgut and salivary gland pose population bottlenecks. By focusing on virus subpopulations in the saliva of multiple mosquito strains, we recapitulated the emergence of a recent epidemic strain of chikungunya and identified E1 glycoprotein mutations with potential to emerge in the future. These mutations confer fitness advantages in mosquito and mammalian hosts by altering virion stability and fusogenic activity. Thus, virus evolutionary trajectories can be predicted and studied in the short term before new variants displace currently circulating strains. [Display omitted] •Analysis of chikungunya virus evolution during natural mosquito-mammal transmission•Emerging strains with epidemic potential identified in mosquito saliva•Viral glycoprotein variants have increased particle stability and fusogenic activity•Variants displace current strain after a single mosquito-to-mammal transmission The ability to follow host-specific evolutionary trajectories of viruses is essential to predict and prevent epidemics. By monitoring chikungunya virus evolution during natural transmission from mosquitoes to mammals, Stapleford et al. recapitulate the emergence events causing a recent epidemic and identify mutations with the potential to emerge in the future.