Diversity and evolution of West Nile virus in Illinois and the United States, 2002-2005

Evolutionary analyses of West Nile virus (WNV) have been limited by uneven sampling across geographic regions and over time. In this study, an expanded data set of 68 WNV envelope gene sequences from the Midwest (Illinois) was created and combined with published sequences to investigate spatial and temporal structuring in the United States viral population. Results indicate an overall lack of geographic structure to WNV in the United States, supporting the notion of WNV as a rapidly expanding pathogen not significantly restricted in its spread by geographic distance. However, analyses of viral genetic diversity show a steady increase in WNV nucleotide-level diversity over time. Additionally, evolutionary rate calculations indicate that WNV has evolved at approximately 0.85 × 10− 3 substitutions/site/year, largely through neutral substitution and purifying selection. Overall, these results show WNV across the United States to be a panmictic viral population that is diversifying and evolving.