West Nile virus (WNV) is similar to other RNA viruses in that it forms genetically complex populations within hosts. The virus is maintained in nature in mosquitoes and birds, with each host type exerting distinct influences on virus populations. We previously observed that prolonged replication in mosquitoes led to increases in WNV genetic diversity and diminished pathogenesis in mice without remarkable changes to the consensus genome sequence. We therefore sought to evaluate the relationships between individual and group phenotypes in WNV and to discover novel viral determinants of pathogenesis in mice and fitness in mosquitoes and birds. Individual plaque size variants were isolated from a genetically complex population, and mutations conferring a small-plaque and mouse-attenuated phenotype were localized to the RNA helicase domain of the NS3 protein by reverse genetics. The mutation, an Asp deletion, did not alter type I interferon production in the host but rendered mutant viruses more susceptible to interferon compared to wild type (WT) WNV. Finally, we used an in vivo fitness assay in Culex quinquefasciatus mosquitoes and chickens to determine whether the mutation in NS3 influenced fitness. The fitness of the NS3 mutant was dramatically lower in chickens and moderately lower in mosquitoes, indicating that RNA helicase is a major fitness determinant of WNV and that the effect on fitness is host specific. Overall, this work highlights the complex relationships that exist between individual and group phenotypes in RNA viruses and identifies RNA helicase as an attenuation and fitness determinant in WNV.West Nile virus (WNV; Flaviviridae: Flavivirus) is a positivesense, single-stranded RNA (ssRNA) virus belonging to the Japanese encephalitis virus (JEV) serological complex of the flaviviruses. WNV perpetuates in nature in enzootic transmission cycles through alternating replication in (mainly avian) vertebrates and mosquitoes. The specific mosquito and avian hosts that are most important in a particular locality differ but tend to include Culex species mosquitoes and passerine birds (2, 10). WNV infection of mammals, including humans and horses, occurs via spillover from this enzootic cycle. Since its introduction into North America in 1999 (20), molecular epidemiologic studies have clearly demonstrated that the virus has evolved to maximize its transmission potential within local transmission cycles (8,11,23). This finding stimulated subsequent efforts to understand the details of the underlying evolutionary mechanisms that lead to population-level genetic and phenotypic changes in the virus. In brief, these studies demonstrated that WNV populations are genetically diverse within hosts (15), that genetic diversity may be shared between hosts (15), and that mosquito infection drives genetic diversification of the virus population both through relaxation of purifying selection and through selection of rare genotypes resulting from RNA interference (RNAi) (4,16,17). Thus, in the WNV transmission cycle, different...