This investigation sought to characterize the shedding of infectious hematopoietic necrosis virus (IHNV) in two populations of Columbia River Basin (CRB) Chinook salmon (Oncorhynchus tshawytscha). Juvenile spring- and fall-run Chinook salmon were exposed by immersion to each of three IHN virus strains from the UC, MD, and L subgroups, and then monitored for viral shedding from individual fish for 30 days. Detectable quantities of UC, MD and L IHN virus were shed by a subset of fish from each host population (1–9 out of 10 fish total in each treatment group). Viral shedding kinetics were consistent, with a rapid onset of shedding, peak shedding by 2–3 days, and then a rapid decline to below detectable levels by 7 days’ post-exposure to IHNV. Intraspecies variation was observed as spring Chinook salmon shed more UC virus than fall fish: spring Chinook salmon shed UC virus in greater numbers of fish, with 22-fold higher mean peak shedding magnitude, 33-fold higher mean total virus shed per fish, and 900-fold higher total virus shed per treatment group. The L and MD viruses had comparable shedding at intermediate levels in each host population. All viral shedding occurred well before host mortality began, and shedding magnitude did not correlate with virulence differences. Overall, the greater shedding of UC virus from spring Chinook salmon, combined with low virulence, indicates a uniquely high transmission potential that may explain the predominance of UC viruses in CRB Chinook salmon. This also suggests that spring-run fish may contribute more to the ecology of IHNV in the CRB than fall-run Chinook salmon.

Theory of the evolution of pathogen specialization suggests that a specialist pathogen gains high fitness in one host, but this comes with fitness loss in other hosts. By contrast, a generalist pathogen does not achieve high fitness in any host, but gains ecological fitness by exploiting different hosts, and has higher fitness than specialists in non-specialized hosts. As a result, specialist pathogens are predicted to have greater variation in fitness across hosts, and generalists would have lower fitness variation across hosts. We test these hypotheses by measuring pathogen replicative fitness as within-host viral loads from the onset of infection to the beginning of virus clearance, using the rhabdovirus infectious hematopoietic necrosis virus (IHNV) in salmonid fish. Based on field prevalence and virulence studies, IHNV subgroups UP, MD, and L are specialists, causing infection and mortality in sockeye salmon, steelhead, and Chinook salmon juveniles, respectively. The UC subgroup evolved naturally from a UP ancestor and is a generalist infecting all three host species but without causing severe disease. We show that specialist subgroups had highest peak and mean viral loads in the hosts in which they are specialized, and they had low viral loads in non-specialized hosts, resulting in large variation in viral load across hosts. Viral kinetics show that the mechanisms of specialization involve both the ability to maximize early virus replication and to avoid clearance at later times, with different mechanisms of specialization evident in different host-virus combinations. Additional nuances in the data included different fitness levels for non-specialist interactions, reflecting different trade-offs for specialist viruses in other hosts. The generalist UC subgroup reached intermediate viral loads in all hosts and showed the smallest variation in fitness across hosts. Evolution of the UC generalist from an ancestral UP sockeye specialist was associated with fitness increases in steelhead and Chinook salmon, but only slight decrease in fitness in sockeye salmon, consistent with low- or no-cost generalism. Our results support major elements of specialist-generalist theory, providing evidence of a specialist-generalist continuum in a vertebrate pathogen. These results also quantify within-host replicative fitness tradeoffs resulting from the natural evolution of specialist and generalist virus lineages in multi-host ecosystems.

Theory of the evolution of pathogen specialization suggests that a specialist pathogen gains high fitness in one host, but this comes with fitness loss in other hosts. By contrast, a generalist pathogen does not achieve high fitness in any host, but gains ecological fitness by exploiting different hosts, and has higher fitness than specialists in non-specialized hosts. As a result, specialist pathogens are predicted to have greater variation in fitness across hosts, and generalists would have lower fitness variation across hosts. We test these hypotheses by measuring pathogen replicative fitness as within-host viral loads from the onset of infection to the beginning of virus clearance, using the rhabdovirus infectious hematopoietic necrosis virus (IHNV) in salmonid fish. Based on field prevalence and virulence studies, IHNV subgroups UP, MD, and L are specialists, causing infection and mortality in sockeye salmon, steelhead, and Chinook salmon juveniles, respectively. The UC subgroup evolved naturally from a UP ancestor and is a generalist infecting all three host species but without causing severe disease. We show that specialist subgroups had highest peak and mean viral loads in the hosts in which they are specialized, and they had low viral loads in non-specialized hosts, resulting in large variation in viral load across hosts. Viral kinetics show that the mechanisms of specialization involve both the ability to maximize early virus replication and to avoid clearance at later times, with different mechanisms of specialization evident in different host-virus combinations. Additional nuances in the data included different fitness levels for non-specialist interactions, reflecting different trade-offs for specialist viruses in other hosts. The generalist UC subgroup reached intermediate viral loads in all hosts and showed the smallest variation in fitness across hosts. Evolution of the UC generalist from an ancestral UP sockeye specialist was associated with fitness increases in steelhead and Chinook salmon, but only slight decrease in fitness in sockeye salmon, consistent with low- or no-cost generalism. Our results support major elements of specialist-generalist theory, providing evidence of a specialist-generalist continuum in a vertebrate pathogen. These results also quantify within-host replicative fitness tradeoffs resulting from the natural evolution of specialist and generalist virus lineages in multi-host ecosystems.

Infectious hematopoietic necrosis virus (IHNV) represents one of the most critical challenges for salmonids in the Pacific Northwest. There are three genogroups of IHNV, designated U, M, and L; the U is further delineated into two subgroups, UC and UP, and the M is further delineated into four subgroups (MA – MD). The UP, UC and MD subgroups co-occur in the Columbia River Basin where the host species sockeye salmon, Chinook salmon, and steelhead trout spawn and rear. Field prevalence data shows that UC viruses exhibit a generalist strategy in Chinook, and steelhead, while two other virus lineages, MD and UP, are more consistent with being specialists in steelhead or sockeye salmon, respectively. The L is found in Northern California and is considered a specialist of Chinook salmon. This study sought to understand early entry and replication of the specialist and generalist IHNV strains in three salmonid hosts. Chinook, steelhead and sockeye were exposed by immersion to their specialist viruses (L, MD and UP, respectively) and to the generalist UC virus. As controls, these hosts were also exposed to buffer (mock control) and IHNV variants that were not specialist for their species (non-specialists). Mortality was monitored throughout the experiments. Fish were sampled at early timepoints post-infection (2, 5, and 8 days post-exposure). Kidney and fin tissues were taken to represent external and internal tissues, respectively. Viral load was assessed by reverse transcriptase quantitative PCR (RT-qPCR) targeting the nucleocapsid (N) gene of IHNV. Additional fish from each experimental group were sampled for histopathology but only a subset were processed and analyzed.

Infectious hematopoietic necrosis virus (IHNV) represents one of the most critical challenges for salmonids in the Pacific Northwest. There are three genogroups of IHNV, designated U, M, and L; the U is further delineated into two subgroups, UC and UP, and the M is further delineated into four subgroups (MA – MD). The UP, UC and MD subgroups co-occur in the Columbia River Basin where the host species sockeye salmon, Chinook salmon, and steelhead trout spawn and rear. Field prevalence data shows that UC viruses exhibit a generalist strategy in Chinook, and steelhead, while two other virus lineages, MD and UP, are more consistent with being specialists in steelhead or sockeye salmon, respectively. The L is found in Northern California and is considered a specialist of Chinook salmon. This study sought to understand early entry and replication of the specialist and generalist IHNV strains in three salmonid hosts. Chinook, steelhead and sockeye were exposed by immersion to their specialist viruses (L, MD and UP, respectively) and to the generalist UC virus. As controls, these hosts were also exposed to buffer (mock control) and IHNV variants that were not specialist for their species (non-specialists). Mortality was monitored throughout the experiments. Fish were sampled at early timepoints post-infection (2, 5, and 8 days post-exposure). Kidney and fin tissues were taken to represent external and internal tissues, respectively. Viral load was assessed by reverse transcriptase quantitative PCR (RT-qPCR) targeting the nucleocapsid (N) gene of IHNV. Additional fish from each experimental group were sampled for histopathology but only a subset were processed and analyzed.

Piscine orthoreovirus genotype one (PRV-1) is the causative agent of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar L.). The virus has also been found in Pacific salmonids in western North America, raising concerns about the risk to native salmon and trout. Here, we report the results of laboratory challenges using juvenile Chinook salmon, coho salmon, and rainbow trout injected with tissue homogenates from Atlantic salmon testing positive for PRV-1 or with control material. Fish were sampled at intervals to assess viral RNA transcript levels, hematocrit, erythrocytic inclusions, and histopathology. While PRV-1 replicated to high loads in all species, there was negligible mortality in any group. We observed a few erythrocytic inclusion bodies in fish from PRV-1 infected groups. At a few time points, hematocrits were significantly lower in the PRV-1 infected groups relative to controls but in no case was anemia noted. The most common histopathological finding was mild, focal myocarditis in both the non-infected controls and PRV-1 infected fish. All cardiac lesions were judged mild and none were consistent with those of HSMI. Together, these results suggest all three species are relatively susceptible to PRV-1 infection, but in no case did infection cause notable disease in these experiments.

Piscine orthoreovirus genotype one (PRV-1) is the causative agent of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar L.). The virus has also been found in Pacific salmonids in western North America, raising concerns about the risk to native salmon and trout. Here, we report the results of laboratory challenges using juvenile Chinook salmon, coho salmon, and rainbow trout injected with tissue homogenates from Atlantic salmon testing positive for PRV-1 or with control material. Fish were sampled at intervals to assess viral RNA transcript levels, hematocrit, erythrocytic inclusions, and histopathology. While PRV-1 replicated to high loads in all species, there was negligible mortality in any group. We observed a few erythrocytic inclusion bodies in fish from PRV-1 infected groups. At a few time points, hematocrits were significantly lower in the PRV-1 infected groups relative to controls but in no case was anemia noted. The most common histopathological finding was mild, focal myocarditis in both the non-infected controls and PRV-1 infected fish. All cardiac lesions were judged mild and none were consistent with those of HSMI. Together, these results suggest all three species are relatively susceptible to PRV-1 infection, but in no case did infection cause notable disease in these experiments.

Throughout a 20-year biosurveillance period, viral hemorrhagic septicemia virus was isolated in low titers from only 6 / 7,355 opportunistically sampled adult Pacific herring, reflecting the typical endemic phase of the disease when the virus persists covertly. However, more focused surveillance efforts identified the presence of disease hot spots occurring among juvenile life history stages from certain nearshore habitats. These outbreaks sometimes recurred annually in the same temporal and spatial patterns and were characterized by infection prevalence as high as 96%. Longitudinal sampling indicated that some epizootics were relatively transient, represented by positive samples on a single sampling date, and others were more protracted, with positive samples occurring throughout the first 10 weeks of the juvenile life history phase. Sampling and biological data associated with these surveillances are presented in this dataset.

Throughout a 20-year biosurveillance period, viral hemorrhagic septicemia virus was isolated in low titers from only 6 / 7,355 opportunistically sampled adult Pacific herring, reflecting the typical endemic phase of the disease when the virus persists covertly. However, more focused surveillance efforts identified the presence of disease hot spots occurring among juvenile life history stages from certain nearshore habitats. These outbreaks sometimes recurred annually in the same temporal and spatial patterns and were characterized by infection prevalence as high as 96%. Longitudinal sampling indicated that some epizootics were relatively transient, represented by positive samples on a single sampling date, and others were more protracted, with positive samples occurring throughout the first 10 weeks of the juvenile life history phase. Sampling and biological data associated with these surveillances are presented in this dataset.

Infectious hematopoietic necrosis virus (IHNV) is an acute pathogen of salmonids in North America, Europe and Asia that is phylogenetically classified into five major virus genogroups (U, M, L, E and J). The geographic range of the U and M genogroup isolates overlap in the North American Columbia River Basin and Washington Coast region, where these genogroups pose different risks depending on the species of Pacific salmon (Oncorhynchus spp.). For certain management decisions, there is a need to both test for IHNV presence and rapidly determine the genogroup. Herein, we report the development and validation of a U/M multiplex reverse transcription, real-time PCR (RT-rPCR) assay targeting the IHNV nucleocapsid (N) protein gene. The new U/M RT-rPCR is a rapid, sensitive, and repeatable assay capable of specifically discriminating between North American U and M genogroup IHNV isolates. However, one M genogroup isolate obtained from commercially cultured Idaho rainbow trout (O. mykiss) showed reduced sensitivity with the RT-rPCR test, suggesting caution may be warranted before applying RT-rPCR as the sole surveillance test in areas associated with the Idaho trout industry. The new U/M assay had high diagnostic sensitivity (DSe > 94%) and specificity (DSp > 97%) in free-ranging adult Pacific salmon, when assessed relative to cell culture (reference standard) and the previously validated universal N RT-rPCR. The good diagnostic performance of the new U/M assay indicates the new test is suitable for surveillance, diagnosis, and confirmation of IHNV in Pacific salmon from the Pacific Northwest regions where the U and M genogroups overlap.