32 - West Nile genomics in the Southwest

Abstract: Since the first detection of West Nile virus (WNV) in the US in 1999, nearly 55,000 people have tested positive and more than 2,700 have died. The overarching goal of our research endeavors is to identify local, regional, and national hotspots that allow for viral maintenance in the environment and could be focused on for targeted mitigation efforts. Over the course of this study, we have had the opportunity to monitor the longest-lasting county-level endemic clade since WNV was first detected in the country. The fall of this WN02 clade in Maricopa County coincides with weather conditions over the past two years - 2023 and 2024 were the hottest years ever recorded in the Phoenix Metropolitan Area. This large endemic clade was replaced by a variant of WNV that is still part of the WN02 genotype, although the two have been genetically distinct since around 2008. The latest variant may behave differently, from a clinical perspective, given amino acid substitutions that have been experimentally shown to have an attenuated phenotype in other flaviviruses. We additionally hypothesized that Maricopa County and Utah mosquito abatement districts have been dealing with the same variants of WNV, given bird flyways shared between the two states. However, the Salt Lake City Metropolitan Area is home to a WN02 clade that has been genetically distinct from the Maricopa County clade since just shortly after the virus entered the US, calling into question the impact of ecological factors that may result in barriers to WNV transmission. Finally, network analyses have revealed that a limited number of locations in heavily sampled areas contribute to viral maintenance over time.