Re-emergence of vesicular stomatitis in the western United States is associated with distinct viral genetic lineages.

Phylogenetic analysis of partial phosphoprotein and glycoprotein gene sequences showed that a single genetic lineage of vesicular stomatitis virus (VSV) serotype New Jersey (NJ) caused the 1995 and 1997 outbreaks of vesicular stomatitis (VS) in the western United States. While distinct from VSV-NJ strains causing previous outbreaks in the western United States and those circulating in feral swine in the southeastern United States, this lineage was closely related to viral lineages circulating in the Mexican states of Guerrero, Veracruz, and Oaxaca in 1996, 1989, and 1984 respectively. In 1997 and 1998, VSV serotype Indiana 1 (IN1) re-emerged in the western United States after 30 years. Viruses causing these outbreaks grouped within a single genetic lineage distinct from VSV-IN1 isolates causing outbreaks in the western United States in 1929 and 1956 but closely related to a strain circulating in the state of Colima in central Mexico in 1997. Our data showed that sporadic VS outbreaks in the western United States are caused by genetically distinct viral lineages closer to those circulating in enzootic areas of central and southern Mexico than to those causing previous outbreaks in the United States. The genetic evidence and temporal distribution of outbreaks are not consistent with a pattern of long-term maintenance of VSV in the western United States.