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Research Project: Ecology of Vesicular Stomatitis Virus (VSV) in North America

Location: Foreign Animal Disease Research

2020 Annual Report


Objectives
1. Ascertain the viral ecology of disease and factors mediating the emergence of VSV, including the characterizing epidemiological factors associated with the maintenance of disease in endemic versus non-endemic settings (ABADRU) and (FADRU), determining the environmental conditions that influence vector dominance in endemic versus non-endemic settings, and identifying environmental-vector interactions responsible for the emergence of viral infections in new geographical locations. 1.A. Characterize epidemiological, biotic and abiotic factors associated with the emergence and transmission of VSV in endemic versus non-endemic settings. 2. Develop intervention strategies to minimize the impact of VSV disease outbreaks. 2.A. Develop means to detect and characterize emergent VSV strains and use these data to generate models that predict future outbreaks. 2.B. Identify vector transmission control strategies based on our understanding of vector-host interactions. 3. Ascertain the viral ecology of disease and factors mediating the emergence of VSV, including factors associated with the maintenance of disease, determining the environmental conditions that influence vector dominance in endemic versus non-endemic settings, and identifying environmental-vector interactions responsible for the emergence of viral infections in new geographical locations. 4. Establish research program on Crimean Congo Hemorrhagic Fever (CCHF) and Nipah Virus Disease (NiVD), including development of detection and diagnostic in vectors and hosts as well as studying mechanisms of inter-species transmission.


Approach
1. A comprehensive analysis of VS outbreaks occurring in the U.S. from 2004-2016 will be conducted to determine the relationship between the geographical location of premises reporting VS outbreaks and the spatial and temporal variability in a large suit of ecological variables. Multiple data streams involving disease occurrence and ecological conditions will be obtained from multiple sources and harmonized for integration and analysis. These data sources include; a) outbreak occurrence data inclusive of geo-location, host species, number of animals affected and onset date, b) ecological data analysis c) biotic and abiotic variables inclusive of animal density, hydrological features and streams, elevation and surface water properties, air temperature and precipitation, vegetation ENSO (El Nino Southern Oscilation) data, soil properties and long term trends in environmental variables. . These data will be harmonized and univariate and multivariate statistical analysis will be conducted to determine the best set of explanatory variables for temporal and spatial patterns. These analyses will be used to identify ecological variables associated with VS disease occupancy and spread in the western U.S. and to develop predictive models for disease spread. 2. The characterization of VSV transmission in endemic vs non-endemic settings will be conducted in collaboration with Mexico’s SENASICA-EADC laboratory to conduct genomic sequencing and phylogeographic characterization of viral strains collected through VS surveillance activities in Mexico and to identify the ecological and environmental factors associated with the occurrence of VSV in Mexico. A collaboration with USDA-APHIS will established to determine the phylogeopraphic characteristics of VSV strains causing outbreaks in the U.S. This information will be used to create predictive models for VSV occurrence. 3. A comprehensive analysis of VS outbreaks occurring in the U.S. will be conducted to determine the relationship between geographical location of premises reporting VS outbreaks and spatial and temporal variability in a large suit of ecological variables. Ecology studies in the sw US will be expanded to include endemic areas in Mexico and environmental-vector interactions responsible for the emergence of viral infections in new geographical locations. These data will be harmonized and statistical analysis will be conducted to determine the best set of explanatory variables for temporal and spatial patterns. These analyses will be used to identify ecological variables associated with VS disease emergence, re-emergence and spread in the western U.S. and to develop predictive models for disease spread. 4. A new research program will be started at the Centers for Disease Control and Prevention on CCHF and NiVD. Research scientists will be embedded within existing research programs to develop expertise working in biosafety level 4 facility, develop necessary reagents and methodologies for studying virus host interaction in livestock species. Initial work will focus on molecular detection tools, reverse genetics systems, immunological reagents for studies in small animal models.


Progress Report
Despite multiple setbacks this year associated with personnel constraints and negative impacts of COVID-19, progress was made on this research project. For Objective 1 “Ascertain the viral ecology of disease and factors mediating the emergence of Vesicular Stomatitis Virus (VSV), including the characterizing epidemiological factors associated with the maintenance of disease in endemic versus non-endemic settings” one manuscript was published in Ecosphere described the advances made on predictive biology of VS in North America, based on 2004-2006 and 2012-2015 VS outbreaks. The models described were applied to the 2019-2020 outbreaks and were able to predict the main regions that became affected. The model will continue to be educated with new data (i.e., machine learning) and we hope to gain higher accuracy in predicting outbreaks in the future. As an extension of this project, a similar model is being applied to West Nile virus occurrence in horses and humans. Under Objective 2, “Develop intervention strategies to minimize the impact of VSV disease outbreaks”, one manuscript was published in the Journal of Equine Veterinary Science that provided an illustrated guide to VS management for horse owners and veterinarians. Under Objective 3 “Ascertain the viral ecology of disease and factors mediating the emergence of VSV…” one manuscript was submitted to Journal Evolutionary Applications addressing relationship between genetic lineages of VSV and specific environmental conditions in the western U.S. Under Objective 4 “A new research program will be started at the Centers for Disease Control and Prevention on Crimean-Congo Hemorrhagic Fever (CCHF) and Nipah Virus Disease (NiVD). Research scientists will be embedded within existing research programs to develop expertise working in Biosafety Level 4 facility.” We successfully established cooperative research agreements with the Centers for Disease Control (CDC) and the University of California-Davis with the aim of training research fellows on BSL4 research focusing on Crimean Congo Hemorrhagic fever virus. As a result, we have two postdoctoral fellows currently embedded at the CDC Special Pathogens Branch and one postdoctoral fellow embedded at the One Health Institute, School of Veterinary Medicine, University of California Davis. These research fellows were being trained in BSL4 research at CDC and field ecology of CCHF in Africa respectively. However, due to the COVID pandemia, they do not have access to the laboratory for field study sites. Therefore, they have been doing literature research and one manuscript was published in Tropical Medicine and Infectious Disease addressing focal areas and gaps in knowledge of Crimean–Congo Hemorrhagic Fever was accepted for publication in the journal.


Accomplishments
1. Predicting vesicular stomatitis virus occurence. Vesicular stomatitis (VS) is a recurring emerging vector-borne viral disease with incursions into the western United States at 8-10 year intervals from endemic areas in Mexico which causes trade disruptions and loses to the horse and livestock industries. Predicting the drivers of disease incursion and expansion as part of early-warning strategies (EWS) is a major challenge for diseases where spread is mediated by climate and other environmental drivers. Under a “Grand Challenge" project, ARS researchers from multiple locations (Manhattan, Kansas; Fort Collins, Colorado; Cheyenne, Wyoming; Las Cruces, New Mexico; and Plum Island, New York) applied a multi-scale big data–model integration approach using human-guided machine learning to evaluate the importance of over 400 environmental variables to develop EWS for VS. VS occurrence at the local scale of individual landowners was related to distance to running water, host density, vegetation, and environmental conditions such as rainfall, temperatures and streamflow. Development of EWS allows predictions of conditions that favor VS incursion and expansion, thereby providing implementation of preventative measures at the local and regional levels.


Review Publications
Velazquez-Salinas, L., Pauszek, S.J., Rodriguez, L.L. 2019. Complete genome sequence of a representative vesicular stomatitis New Jersey virus strain (NJ03CPB) from an endemic region of southern Mexico. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.00499-19.
Peck, D.E., Reeves, W.K., Pelzel-McCluskey, A.M., Derner, J.D., Drolet, B.S., Cohnstaedt, L.W., Swanson, D.A., McVey, D.S., Rodriguez, L.L., Peters, D.C. 2020. Management strategies for reducing the risk of equines contracting Vesicular Stomatitis Virus (VSV) in the Western United States. Journal of Equine Veterinary Science. 90:103026. https://doi.org/10.1016/j.jevs.2020.103026.
Peters, D.C., McVey, D.S., Elias, E.H., Pelzel-McCluskey, A.M., Derner, J.D., Burruss, N., Schrader, T.S., Yao, J., Pauszek, S.J., Lombard, J., Rodriguez, L.L. 2020. Big data-model integration and AI for vector-borne disease prediction. Ecosphere. 11:1-20. https://doi.org/10.1002/ecs2.3157.
Velazquez-Salinas, L., Verdugo-Rodriguez, A., Rodriguez, L.L., Borca, M.V. 2019. The role of interleukin 6 during viral infections. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.01057.