Genetics Reveal Long-Distance Virus Transmission Links in Pacific Salmon

SIMPLE SUMMARY: The transmission of viruses between host populations is essential for viruses to persist on the landscape. Therefore, the identification of specific transmission links can provide insights into how a virus moves from source to recipient (sink) populations, allowing for the development of strategies to interrupt transmission routes and control viral disease. For the fish pathogen infectious hematopoietic necrosis virus (IHNV), this study identifies three transmission links associated with the emergence of IHNV in coastal Washington steelhead trout populations between 2007 and 2011. The links were identified by the genetic typing of virus isolates obtained from coastal fish and potential source fish from the Columbia River Basin. Three exact genotype matches were found, indicating at least three introductions of virus from Columbia fish to coastal fish during years of the emergence event. Likely sources were juvenile fish in the Columbia region experiencing disease, and the first detected recipient populations in all cases were adult fish returning to coastal hatcheries. Variation in timing and distance for these three transmission links will provide Pacific Northwest fish health managers with a better understanding of IHNV transmission routes from Columbia region fish to coastal steelhead trout. ABSTRACT: In the coastal region of Washington State, a major pathogen emergence event occurred between 2007 and 2011 in which steelhead trout (Oncorhynchus mykiss) experienced a high incidence of infection and disease outbreaks due to the rhabdovirus infectious hematopoietic necrosis virus (IHNV). Genetic typing showed that the introduced viruses were in the steelhead-specific MD subgroup of IHNV and indicated the most likely source was a virus from the nearby Columbia River Basin. In the current study, full-length viral glycoprotein (G) gene sequences were determined for 55 IHNV isolates from both coastal and Columbia fish populations to identify specific source populations and infer mechanisms of transmission to coastal steelhead. We identified three transmission links based on exact fullG genotype matches between Columbia and coastal fish. In all cases, the likely source population was infected juvenile fish, and sink populations were adult fish returning to coastal rivers to spawn. The time intervals between detection in source and sink populations varied from 6 months to nearly 4 years, suggesting different transmission pathways. Surprisingly, distances between source and sink populations varied between 140 and 1000 km. These results confirm repeated introductions of virus from Columbia River Basin fish as the cause of emergence of MD virus on the Washington coast from 2007 to 2011.