viruses Article Virulence and Infectivity of UC, MD, and L Strains of Infectious Hematopoietic Necrosis Virus (IHNV) in Four Populations of Columbia River Basin Chinook Salmon Daniel G. Hernandez 1,2, William Brown 3 , Kerry A. Naish 2 and Gael Kurath 1,* 1 Western Fisheries Research Center, United States Geological Survey, Seattle, WA 98115, USA; [email protected] 2 School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA; [email protected] 3 Department of Statistics, University of Washington, Seattle, WA 98195, USA; [email protected] * Correspondence: [email protected] Abstract: Infectious Hematopoietic Necrosis Virus (IHNV) infects juvenile salmonid fish in conserva- tion hatcheries and aquaculture facilities, and in some cases, causes lethal disease. This study assesses intra-specific variation in the IHNV susceptibility of Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River Basin (CRB), in the northwestern United States. The virulence and infectivity of IHNV strains from three divergent virus genogroups are measured in four Chinook salmon popula- tions, including spring-run and fall-run fish from the lower or upper regions of the CRB. Following controlled laboratory exposures, our results show that the positive control L strain had significantly higher virulence, and the UC and MD strains that predominate in the CRB had equivalently low virulence, consistent with field observations. By several experimental measures, there was little variation in host susceptibility to infection or disease. However, a small number of exceptions Citation: Hernandez, D.G.; Brown, suggested that the lower CRB spring-run Chinook salmon population may be less susceptible than W.; Naish, K.A.; Kurath, G. Virulence other populations tested. The UC and MD viruses did not differ in infectivity, indicating that the and Infectivity of UC, MD, and L observed asymmetric field prevalence in which IHNV detected in CRB Chinook salmon is 83% UC Strains of Infectious Hematopoietic and 17% MD is not due to the UC virus being more infectious. Overall, we report little intra-species Necrosis Virus (IHNV) in Four Populations of Columbia River Basin variation in CRB Chinook salmon susceptibility to UC or MD IHNV infection or disease, and suggest Chinook Salmon. Viruses 2021, 13, 701. that other factors may instead influence the ecology of IHNV in the CRB. https://doi.org/10.3390/v13040701 Keywords: virulence; infectivity; infectious hematopoietic necrosis virus; IHNV; infectious dose; Academic Editor: Kyle A. Garver Columbia River Basin; Chinook salmon; intraspecies variation Received: 23 February 2021 Accepted: 14 April 2021 Published: 18 April 2021 1. Introduction The aquatic rhabdoviral pathogen infectious hematopoietic necrosis virus (IHNV) Publisher’s Note: MDPI stays neutral infects many species of Pacific salmonid fish. In the multi-host ecosystems of western North with regard to jurisdictional claims in American rivers, IHNV has diverged into three major virus genogroups that vary in host- published maps and institutional affil- specific virulence for three major host species: Chinook salmon (Oncorhynchus tshawytscha), iations. sockeye salmon (O. nerka), and steelhead/rainbow trout (both O. mykiss)[1,2]. In the large Columbia River Basin (CRB) of the US Pacific Northwest, the most abundant host is Chinook salmon, and recent studies suggest that subclinical infection of Chinook salmon with IHNV may be contributing to the transmission and maintenance of the virus across the Copyright: © 2021 by the authors. watershed [3,4]. Chinook salmon occur in the CRB as numerous distinct sub-populations Licensee MDPI, Basel, Switzerland. and exhibit dramatic variation in life-history phenotypes. The dominant Chinook salmon This article is an open access article life-history phenotypes in the CRB are known as spring-run and fall-run Chinook salmon, distributed under the terms and which differ in many ecologically important traits, including spatial ranges (Figure1) and conditions of the Creative Commons seasonal timing of both juvenile seaward migration and adult upstream migration for Attribution (CC BY) license (https:// spawning [5,6]. Phylogenetic analyses of CRB Chinook salmon by various methods have creativecommons.org/licenses/by/ 4.0/). revealed three or four clearly distinct genetic lineages that vary in geographic distribution Viruses 2021, 13, 701. https://doi.org/10.3390/v13040701 https://www.mdpi.com/journal/viruses Viruses 2021, 13, x 2 of 27 Viruses 2021, 13, 701 ranges (Figure 1) and seasonal timing of both juvenile seaward migration and adult up-2 of 25 stream migration for spawning [5,6]. Phylogenetic analyses of CRB Chinook salmon by various methods have revealed three or four clearly distinct genetic lineages that vary in geographic distribution and life-history phenotypes [6–9]. To date, variation in host spec- and life-history phenotypes [6–9]. To date, variation in host specificity of IHNV has been ificity of IHNV has been defined at the host species level, but potential differences in the defined at the host species level, but potential differences in the interactions of IHNV with interactions of IHNV with different life-history phenotypes or phylogenetic lineages of different life-history phenotypes or phylogenetic lineages of CRB Chinook salmon have CRB Chinook salmon have not been explored. The goal of this investigation was to test not been explored. The goal of this investigation was to test for intraspecies variation in forthe intraspecies susceptibility variation of CRB in Chinook the susceptibility salmon populations of CRB Chinook to infection salmon and populations disease following to in- fectionexposure and todisease distinct following strains ofexposure IHNV. Here, to distinct we measured strains of the IHNV. virulence Here, and we infectivity measured of thethree virulence IHNV strainsand infectivity representing of relevant three virusIHNV genogroups, strains representing in four diverse relevant populations virus of genogroups,CRB Chinook in salmon,four diverse including populations spring- of and CRB fall-run Chinook populations salmon, from including the upper spring- and and lower fall-runregions populations of the watershed. from the By upper combining and lower results regions of controlled of the watershed. laboratory By exposures combining with resultsfield surveillanceof controlled data, laboratory we assessed exposures factors with of field both surveillance the host and data, virus, we leading assessed to observedfactors ofpatterns both the of host IHNV and infection virus, leading and virulence to observed in CRB patterns Chinook of IHNV salmon. infection Together, and this virulence investiga- in tionCRB aimed Chinook to better salmon. understand Together, the this contributions investigation of aimed distinct to Chinookbetter understand salmon populations the con- tributionsto the ecology of distinct and epidemiologyChinook salmon of IHNV populations across the to Columbiathe ecology River and Watershed.epidemiology of IHNV across the Columbia River Watershed. (a) (b) FigureFigure 1. Maps 1. Maps of the of Columbia the Columbia River River Basin Basin(outlined (outlined in grey) in of grey) the northwestern of the northwestern United States United and States southwestern and southwestern Canada showingCanada rivers showing and rivers streams and streams(green lines) (green containing lines) containing spring-run spring-run (a) and (a )fall-run and fall-run (b) populations (b) populations of Chinook of Chinook Salmon. Salmon. Spring-runSpring-run Chinook Chinook salmon salmon migrate migrate to tothe the upper, upper, interior interior reaches reaches of ofthe the basin basin and and spawn spawn in insmaller smaller tributary tributary streams, streams, whereas fall-run salmon spawn in larger, mainstem rivers. The lower Columbia Basin (“Low”) lies west of the Cascade whereas fall-run salmon spawn in larger, mainstem rivers. The lower Columbia Basin (“Low”) lies west of the Cascade Mountain Range, and the upper Columbia Basin (“Up”) lies east of the Cascade Mountains. Spatial distributions of the Mountain Range, and the upper Columbia Basin (“Up”) lies east of the Cascade Mountains. Spatial distributions of the Chinook salmon populations were sourced from StreamNet GIS Data [10]. Source locations for the four Chinook salmon populationsChinook salmon tested here populations are shown. were sourced from StreamNet GIS Data [10]. Source locations for the four Chinook salmon populations tested here are shown. IHNV is an enveloped, single-stranded, negative-sense RNA virus (species Salmonid IHNV is an enveloped, single-stranded, negative-sense RNA virus (species Salmonid novirhabdovirus) belonging to the taxonomic family Rhabdoviridae, in the genus No- novirhabdovirus) belonging to the taxonomic family Rhabdoviridae, in the genus Novirhab- virhabdovirus [11–13]. IHNV can cause high mortality in juvenile salmonids in conserva- dovirus [11–13]. IHNV can cause high mortality in juvenile salmonids in conservation tion hatcheries and commercial aquaculture facilities, and disease impacts have been well hatcheries and commercial aquaculture facilities, and disease impacts have been well documented in rainbow trout and steelhead trout (freshwater and anadromous forms O. documented in rainbow trout and steelhead trout (freshwater and anadromous forms O. mykiss), sockeye salmon, and Chinook salmon [11,12]. Genetic typing and phylogenetic mykiss), sockeye salmon, and Chinook salmon [11,12].