Research Project: Predicting and Mitigating Vesicular Stomatitis Virus (VSV) Outbreaks in North America

Location: Foreign Arthropod Borne Animal Disease Research

2023 Annual Report

Objectives
Objective 1: Ascertain the viral ecology and factors mediating the introduction and expansion of VSV in the U.S. Objective 1A. Identify viral genetic determinants mediating emergence of epidemic VSV in the U.S. as well as adaptation to insect and animal hosts. Objective 1B. Characterize epidemiological, biotic and abiotic factors associated with vectorial capacity, emergence, incursion, and expansion of VSV from endemic areas into the U.S. Objective 2. Develop intervention strategies to minimize the impact of VSV disease outbreaks. Objective 2A. Retrospectively integrate and harmonize environmental, vector, host, and viral variables with disease occurrence data to support the development of predictive multi-scale big data models for VSV. Objective 2B. Develop model-based early warning systems to predict future incursions of VSV from Mexico to the U.S. Objective 2C. Identify vector transmission control strategies based on our understanding of virus-vector-host interactions.

Approach
Objective 1A:The effect of genetic changes on virulence and transmissibility will be investigated with three approaches: 1) investigating virulence in pigs and vector transmissibility in relevant vectors (e.g., midges and black flies); 2) characterizing genomes of the 2019-2020 VSIV U.S. epidemic strains using comparative genomics to identify genetic differences between epidemic and endemic VSIV in Mexico. 3) if different endemic vs. epidemic lineages are identified, then characterize the virulence of these strains. Objective 1B. We will quantify the occurrence of VS cases across space and time in the endemic region in Mexico. Together these data will enable us to quantify the occurrence of VS cases across space and time in the endemic region. If successful, we expect to identify associations between VS cases and environmental/ecological factors. We will employ the big data model integration (BDMI) approach used previously by our VSV-GC collaborators. Objective 2A: Temporal relationships between VS occurrences and variables representing environmental factors relevant to VS transmission will be evaluated. First, municipality level VS occurrence data from 1981 – 2020 provided by SENASICA will be temporally binned based on incursion years into the U.S.: 1985, 1995, 2004, 2012, or 2019. Next, collated datasets representing environmental, ecological and/or biological factors relevant VS occurrences across Mexico for each year identified from Goal 1B.1 will be synchronized with the SENASICA dataset. Initially, time-series analysis of VS occurrence within temporal bins across geographic space will be performed. This analysis will help determine whether VS occurrence and spread outside of the endemic region occurs randomly or non-randomly in space and time prior to incursion in the U.S. We will then test whether identified factors reliably predict incursions to the U.S. using multivariate analyses and, if appropriate, machine learning as previously described. Analyses may reveal genomic markers of virulence to inform surveillance in Mexico and early warning programs. If successful, we expect to identify a reliable set of environmental/ecological/biological variables that can be used to inform early warning metrics in predictive modeling of VSV incursion. Objective 2B: We hypothesize that VSV infection will alter photosensory perception, altering the effectiveness of current phototaxis-dependent surveillance traps and management strategies. If successful, we will determine the effects of VSV infection on midge photoattraction behavior and on the expression of vision or other neurosensory genes.

Progress Report
Substantial overall progress was made in this research project addressing all the objectives during FY 2023. An important event occurred in 2023: the incursion of Vesicular Stomatitis New Jersey virus (VSNJV) in the United States, specifically in California. This represented an opportunity to collaborate with Animal and Plant Health Inspection Service – National Veterinary Services Laboratories (APHIS-NVSL) in the genomic characterization and determine the phylogeographic origin of the new Vesicluar Stomatitis Virus (VSV) incursion. The results of these studies are ongoing and will be reported in FY 2024. We have continued to collaborate within the Grand Challenge partners (APHIS), SciNet, and continued partnerships with New Mexico State University, Colorado State University, Kansas State University, and the Animal Health Service in Mexico (SENASICA). Objective 1A. An important accomplishment was the successful in-vivo characterization of the infectious-clone derived VSNJV epidemic lineage 1.1 containing the 5 most significant amino acid mutations found in endemic lineage 1.2. This mutant virus was compared to its wild-type progenitor for its virulence in our previously established pig inoculation model. The results showed clear differences in virus shedding between these viruses that might suggest mechanisms of emergence and spread of the epidemic viral lineage. Further studies are in progress. In addition, through a collaboration with Kansas State University, we initiated a molecular pathogenesis study aimed at determining the cellular host proteins required for efficient growth of VSV in mammalian cells. There were 5 candidate host factors identified that seem to influence the virus to reproduce in cells. The identification of host factors involved in the VSV replication cycle will increase our knowledge of the molecular pathogenesis of the virus and influence the development of potential antivirals. During the 2019-2020 Vesicular Stomatitis Indiana Virus (VSIV) outbreaks there was great progress made under a collaborative agreement with Colorado State University, we finalized the genomic analysis of over 100 near – full length genomes of VS Indiana (VSIV) viruses from Colorado, Texas, New Mexico, Kansas, Missouri, Nebraska, and Wyoming, and showed the genetic diversity associated with each of the years and geographical areas of the 2019-2020 outbreaks. This represents the most extensive and comprehensive analysis of VSIV to date and demonstrated that a single incursion of a viral lineage from Mexico was the origin of the outbreak. In May 2023, APHIS’s National Veterinary Services Laboratories (NVSL), confirmed a case of VSNJV on an equine premises in San Diego County, California. This is the first report of VSV in California in over three decades. In collaboration with NVSL colleagues, ARS scientists in Orient Point, New York, and Manhattan, Kansas, determined the origin of the outbreak causing strain and tracked it to a viral genetic lineage (lineage 2.2) of Central American origin that was detected circulating in Mexico as early as 2008, as documented in a manuscript published in 2012. We identified this lineage as of concern as it represented a new introduction of this virus into Mexico with the potential of expanding into the U.S. Furthermore, this epidemic lineage affected the San Diego Safari Park where 21 specimens from two species of rhinoceros (Asian and African) were clinically affected, some of them severely. ARS scientists are collaborating with APHIS, the safari park scientists and clinical veterinarians to control the disease in affected animals. Additional studies are being carried out at the safari park including serological sampling of other animal species to determine the extent of animal species infected and sampling of insects to determine the potential vectors spreading the virus in and around the safari park. Objective 1B. Through an agreement with New Mexico State University (NMSU) we continued research activities in Chiapas, Mexico in collaboration with Mexico’s National Animal Health Service SENASICA. A study to elucidate the spatiotemporal dynamics of different VSV vectors (black flies, sand flies, midges, and mosquitoes) on five farms in the State of Chiapas, has made great progress, with thousands of insects captured at the five sites. Further, testing of the insects by real-time Polymeras Chain Reaction (rt-PCR) at the Mexico laboratory yielded a number of virus-positive insect pools for both VS New Jersey and Indiana serotypes of VSV. In addition, clinical cases of VSV were reported and characterized by the central laboratory in Mexico yielding positive results for virus detection. These samples were shipped to the ARS laboratory at Plum Island, New York, for further characterization and genomic sequencing. In addition, a long-term dataset on all reported VSV cases over the last thirty years is being analyzed, along with remotely sensed data on climate, land cover/land use, and distribution of domestic animals and has identified key variables regarding the distribution of VSV within its endemic range. This study is nearing completion. Finally, a current research collaboration with Mexico will be expanded to include two additional study sites in Central and Northern Mexico. The aim of this new project is to document the expansion of epidemic strains of VSV within Mexico to inform the development of predictive models for the occurrence of VSV epidemics in the U.S. Objective 2A. During the past year a detailed analysis of the 2014-2015 VSNJV outbreak and 2019-2020 VSIV is being carried out through collaborations within the ARS Grand Challenge synergy project. It was determined that for the 2019-202 VSIV outbreak there were distinct viral lineages during the incursion year in Colorado and New Mexico compared to the expansion years in multiple States (Kansas, Nebraska, Missouri, Wyoming). The genetic data as well as environmental variables are being used to refine the predictive models previously developed for VSNJV. An abstract entitled “The relationship between broad-scale climate variability and the expansion of a vector-borne disease in North America” describing this effort was presented at the Spatial Statistics 2023 meeting.

Accomplishments
1. The role of innate immune response in Vesicular Stomatitis Virus (VSV) pathogenesis: Applications to animal and public health. Innate immunity is key to the prevention and control of viral disease. Vesicular stomatitis has been previously used to study innate responses, particularly interferon induction and response pathways. In addition to being a disease-causing virus, VSV is being utilized as an effective vaccine viral vector (e.g., Ebola virus vaccine) and as a cancer treatment as an oncolytic agent. ARS scientists in Orient, New York, and Manhattan, Kansas, previously reported that a single amino-acid substitution in one protein (M51R) of Vesicular Stomatitis New Jersey Virus (VSNJV) has a fully attenuating effect in a natural host (pigs) with attenuation being mediated by the inability of this mutant to shut down host innate immune response. Here ARS researchers further characterized the gene expression of cells infected with M51R compared to the wild type progenitor virus. The results showed that the cells infected with mutant virus expressed significantly higher levels of multiple interferon and other innate response genes within the innate response and cell-death pathways. The identification of the cellular genes regulated by VSV will inform the development of better antiviral treatments, improved vaccines, and safer and effective targeted cancer treatment options. This research is a good example of cross-cutting science applied to multiple fields in animal and public health.

Review Publications
Bertram, M.R., Rodgers, C., Reed, K., Velazquez Salinas, L., Pelzel-Mccluskey, A., Mayo, C., Rodriguez, L.L. 2023. Vesicular stomatitis Indiana virus near-full-length genome sequences reveal low genetic diversity during the 2019 outbreak in Colorado, USA. Frontiers in Veterinary Science. 10. Article 1110483. https://doi.org/10.3389/fvets.2023.1110483.
Leon, B., Sanchez, C., Rodriguez, L.L., Cordero-Solorzano, J.M. 2022. Vesicular stomatitis virus isolated from a bovine brain sample in Costa Rica. Microbiology Resource Announcements. https://doi.org/10.1128/mra.00737-22.
Velazquez Salinas, L., Medina, G.N., Valdez, F., Collinson, S., Zarate, S., Zhu, J.J., Rodriguez, L.L. 2023. Exploring the molecular basis of vesicular stomatitis virus pathogenesis in swine: insights from expression profiling of primary macrophages infected with M51R mutant virus. Pathogens. 12(7). Article 896. https://doi.org/10.3390/pathogens12070896.