Genetic diversity, evolution, and fitness of infectious hematopoietic necrosis virus within an endemic focus in rainbow trout aquaculture
The rhabdovirus infectious hematopoietic necrosis virus (IHNV) is the most significant viral pathogen of salmon and trout in North America. The virus infects wild, hatchery, and farmed fish populations from Alaska to California and inland to Idaho, causing disease with up to 90% mortality. In the 41 mile Hagerman Valley of Idaho, IHNV is endemic among numerous rainbow trout farms and resource mitigation hatcheries. In this work, the genetic diversity of IHNV in the Hagerman Valley was characterized at multiple levels using RNase protection assays (RPA) of the entire viral glycoprotein (G) gene and nucleotide sequencing of a 303 nucleotide region of the G gene. Characterization of 122 virus isolates from 18 rainbow trout farms and three state fish hatcheries demonstrated the presence of multiple virus lineages which appeared to co-circulate among all types of facilities throughout the geographic region. This demonstrated five-fold greater genetic diversity than has been found in other geographic regions, suggesting that conditions specific to rainbow trout aquaculture have accelerated the evolution of IHNV. Virus populations within two individual outbreaks in aquaculture rearing ponds and within four individual rainbow trout had levels of heterogeneity similar to IHNV populations in other environments, suggesting that the forces responsible for increased viral diversity in this environment do not act at the intra-outbreak or intra-host level. In order to assess the relative fitness of IHNV variants in rainbow trout, a novel in vivo competition system was developed. Methods were developed for challenging rainbow trout with two different IHNV genotypes, allowing infection and virus competition within the host to occur, and then subsequently analyzing the virus progeny populations present within each infected fish to determine whether one or both of the genotypes were present and in what proportions. Challenge of 16 fish with two IHNV genotypes from the Hagerman Valley demonstrated the ability of the system to generate and characterize mixed infections, and indicated that the two genotypes were of equal fitness.
- Pathobiology