Interrogating genomes and geography to unravel multiyear vesicular stomatitis epizootics

Authors: Humphreys Jr, John; Shults, Phillip; Velazquez, Lauro; Bertram, Miranda; PELZEL-MCCLUSKEY, ANGELA - Animal And Plant Health Inspection Service (APHIS); Peters, Debra; Rodriguez, Luis; PAUSZEK, STEVEN - Animal And Plant Health Inspection Service (APHIS)

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/9/2024
Publication Date: 7/11/2024
Citation: Humphreys Jr, J.M., Shults, P.T., Velazquez Salinas, L., Bertram, M.R., Pelzel-McCluskey, A.M., Peters, D.C., Rodriguez, L.L., Pauszek, S.J. 2024. Interrogating genomes and geography to unravel multiyear vesicular stomatitis epizootics. Viruses. 16(7). Article 1118. https://doi.org/10.3390/v16071118.
DOI: https://doi.org/10.3390/v16071118

Interpretive Summary: This study aimed to understand how the Vesicular Stomatitis New Jersey virus (VSNJV), a virus that causes livestock disease, spread during the 2014-15 outbreak in the United States. Researchers faced the problem of incomplete virus sampling and varying spatial factors, making it difficult to track the virus accurately. Scientists performed a detailed analysis using genetic data from the virus, confirmed disease cases, and environmental factors. Despite uncertainties, they discovered that the virus likely re-entered the population multiple times and possibly survived the winter. They identified a specific area near the US-Mexico border as the primary source of the virus. This accomplishment contributed to solving the problem by highlighting the need for targeted management practices based on location and time.

Technical Abstract: We conducted an integrative analysis to elucidate the spatial epidemiological patterns of the Vesicular Stomatitis New Jersey virus (VSNJV) during the 2014-15 epizootic cycle in the United States (US). Using georeferenced VSNJV genomics data, confirmed Vesicular Stomatitis (VS) disease cases from surveillance, and a suite of environmental factors, our study assessed environmental and phylogenetic similarity to compare VS cases reported in 2014 and 2015. Despite uncertainties from incomplete virus sampling and cross-scale spatial processes, patterns suggested multiple independent re-invasion events concurrent with potential viral overwintering between sequential seasons. Our findings pointed to a geographically defined Southern Virus Pool at the US-Mexico interface as the source of VSNJV invasions and overwintering sites. Phylodynamic analyses demonstrated an increase in virus diversity before a rise in case numbers and a pronounced reduction in virus diversity during the winter season, indicative of a genetic bottleneck and a significant narrowing of virus variation between the summer outbreak seasons. Environment-vector interactions underscored the central role of meta-population dynamics in driving disease spread. These insights emphasize the necessity for location and time-specific management practices, including rapid response, movement restrictions, vector control, and other targeted interventions.