Whole-Genome Sequences Of Vesicular Stomatitis Virus Isolates From The 2004-2006 US Outbreaks Reveal Evidence of Molecular Adaptation To Ecological Variables

Authors: PALINSKI, RACHEL - US Department Of Agriculture (USDA); PAUSZEK, STEVEN - US Department Of Agriculture (USDA); BURRUSS, DYLAN - US Department Of Agriculture (USDA); SAVORY, HEATHER - US Department Of Agriculture (USDA); HUMPHREYS, JOHN - US Department Of Agriculture (USDA); PELZEL-MCCLUSKEY, ANGELA - Animal And Plant Health Inspection Service (APHIS); Arzt, Jonathan; PETERS, DEBRA - US Department Of Agriculture (USDA); Rodriguez, Luis

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2020
Publication Date: 6/17/2020
Citation: Palinski, R.M., Pauszek, S., Burruss, D.N., Savory, H., Humphreys, J., Pelzel-McCluskey, A.M., Arzt, J., Peters, D., Rodriguez, L.L. 2020. Whole-genome sequences of Vesicular Stomatitis Virus isolates from the 2004-2006 U.S. outbreaks reveal evidence of molecular adaptation to ecological variables. Molecular Ecology. https://doi.org/10.3390/proceedings2020050076.
DOI: https://doi.org/10.3390/proceedings2020050076

Interpretive Summary: Vesicular stomatitis virus (VSV) is an insect-transmitted virus that causes outbreaks of vesicular disease in horses, cattle and pigs. In the western USA outbreaks occur cyclically at approximately 8-10 year intervals. In cattle and pigs the vesicular disease resembles that caused by foot-and-mouth disease virus, a devastating foreign animal disease. The factors mediating the emergence and spread of the virus remain unclear. Previous studies using partial (450 bases) viral genetic sequences, were unable to track the virus distribution and transmission during the 2004-2006 outbreaks. In this study using near full length virus genetic sequences (>10,000 bases) we were able to trace the viral movement from Mexico to southern NM and TX in 2004. Subsequently, in 2005, the virus appeared in 9 states (AZ, CO, ID, MT, NE, NM, TX, UT and WY) and in 2006 VS was detected only in WY. The data analysis suggested that a single VS virus entered the US and caused the 2004 outbreak. this same virus re-emerged in 2005 and 2006. The mechanism of VS emergence and re-emergence remain unclear. However, we found clear associations of specific viruses with environmental conditions. This suggest that different viruses exist in areas with different ecological conditions. Understanding what conditions are necessary for VSV to exist will help device better control methods.

Technical Abstract: Vesicular stomatitis (VS) outbreaks in the western USA occur cyclically approximately every 8-10 years. Historic phylogenetic evidence based on a 450nt region of the P coding sequences suggests that the initial introduction is typically a single viral lineage closely related to those circulating in endemic areas of Mexico. In 2004, a VS outbreak initiated in southern NM and TX and spread as far north as northern CO. Subsequently, in 2005, VS cases appeared in 9 states (AZ, CO, ID, MT, NE, NM, TX, UT and WY) and in 2006 VS was detected only in WY. Phylogenetic analysis suggested that a single VS New Jersey virus (VSNJV) lineage caused the 2004 outbreak, and re-emerged in 2005 and 2006. The mechanism of VS emergence and re-emergence remain unclear. Here, we use near full-length genomic sequences of 60 viral strains isolated from 2000-2006 in the US and Mexico to determine their phylogeographic relationships and environmental variables associated with outbreak dynamics. The results confirmed that a single VSNJV lineage caused the 2004-2006 US outbreaks and its closest ancestor was a virus circulating in Colima, Mexico in 2004. Furthermore, rather than a simple geographic relationship, specific viral genetic sublineages or patristic groups were associated to seasonal environmental variables, particularly evaporative demand, soil moisture, and precipitation. The results suggest a functional role for environmental factors in shaping the evolution and spread of VSNJV in the USA.