The emergence of NY10: Insights into the 2012 West Nile virus outbreak in the United States

Authors: FAUTT, CHAD - Oak Ridge Institute For Science And Education (ORISE); BOUDREAU, MELANIE - Mississippi State University; MOONEY, AMBER - Oak Ridge Institute For Science And Education (ORISE); Cohnstaedt, Lee; Hudson, Amy; Humphreys Jr, John

Submitted to: Virus Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2025
Publication Date: 5/14/2025
Citation: Fautt, C., Boudreau, M.R., Mooney, A.C., Cohnstaedt, L.W., Hudson, A.R., Humphreys Jr, J.M. 2025. The emergence of NY10: Insights into the 2012 West Nile virus outbreak in the United States. Virus Evolution. Article veaf037. https://doi.org/10.1093/ve/veaf037.
DOI: https://doi.org/10.1093/ve/veaf037

Interpretive Summary: West Nile Virus (WNV) is still a human and animal health concern in North America because it can change and adapt quickly. In the U.S., most research has focused on certain genetic changes in the virus (WN02 and SW03), but a different version, called NY10, first found in 2010, has not been studied as much. We looked at the history and spread of NY10 and found that it became more common in the early 2010s. Our research suggests that NY10 played a key role in the 2012 WNV outbreak because it was more genetically diverse than other versions of the virus at the time. However, NY10 has mostly stayed in one region and has not been found west of Colorado, possibly because natural barriers in the southwestern U.S. limit its spread. These findings show how WNV’s evolution, geography, and the environment all interact in complex ways.

Technical Abstract: West Nile Virus (WNV) remains a public health risk across North America due to its capacity for rapid adaptation and evolution. While research in the United States has focused on the WN02 and SW03 mutations, the NY10 genotype, first detected in 2010, has received comparatively little attention. We conducted a phylogenetic and phylodynamic investigation of NY10, revealing its rapid increase in detection frequency and effective population size in the early 2010s. Our analysis suggests that NY10 played an important role in the 2012 WNV outbreak, with an effective population size indicating higher diversity than other lineages during this period. Despite this, NY10 appears geographically restricted, with no detections west of Colorado, indicating that barriers in the southwestern United States may influence its spread. These findings highlight the complex interplay between viral evolution, geography, and the environmental factors that shape WNV epidemiology. The study emphasizes the potential of WNV to generate genotypes with epidemic potential and underscores the importance of integrating genetic data into surveillance and forecasting systems to better predict and manage future outbreaks. Understanding the drivers of WNV’s genetic diversity will be crucial for developing more effective public health strategies as the virus continues to evolve.