Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages

RNA viruses have short generation times and high mutation rates allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for lineage-specific fitness differences. We generated a library of infectious clones representing twelve major Zika virus clades from the epidemic that we used to measure replicative fitness within disease-relevant human primary cells and live mosquitoes. We found that two of the twelve clade-defining nonsynonymous mutations conferred significant in vitro replicative fitness changes among human primary cells, but we did not find evidence for fitness changes in Aedes aegypti mosquitoes. Moreover, we found evidence for elevated levels of positive selection among amino acid sites that define major Zika virus lineages. While our work suggests that Zika virus may have acquired several phenotypic changes during a short time scale, these changes are relatively moderate and do not appear to have enhanced the virulence or transmission of the virus during the epidemic.