West Nile virus strain:WN02 | isolate:FtC-3699 Raw sequence reads

Arthropod-borne viruses (arboviruses), such as Zika, chikungunya, and West Nile virus (WNV), pose as continuous threats to emerge and cause large epidemics. Often these events are associated with novel virus variants optimized for local transmission, which first arise as minorities within a host. Thus the conditions that regulate the frequency of intrahost variants are important determinants of emergence. Here we describe the dynamics of WNV genetic diversity during its transmission cycle. Virus populations expectorated in mosquito saliva are highly diverse and unique to each feeding episode, demonstrating the significant adaptive potential that can rapidly change through time. During transmission to birds, however, most genetic diversity is removed by strong purifying selection. Further, transmission of potentially mosquito-adaptive WNV variants is strongly influenced by genetic drift in mosquitoes. These results highlight the complex evolutionary forces that a novel virus variant must overcome to alter infection phenotypes at the population level.