Molecular indices of viral disease development in wild migrating salmon†

Miller, Kristina M.; Günther, Oliver P.; Li, Shaorong; Kaukinen, Karia H.; Ming, Tobi J.

doi:10.1093/conphys/cox036

Cited by 76 publications

(136 citation statements)

References 72 publications

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“…Nucleic acids (DNA and cDNA) obtained from liver samples were assessed for 45 salmonid infectious agents (12 viruses, 11 bacterial pathogens and 22 microparasites) using 46 qPCR assays and a single host reference gene (hkg; S100 calcium binding protein (78d16.1) as described in Miller, Gunther, Li, Kaukinen, & Ming, ) run on the BioMark platform. All the assays included on the BioMark platform are for agents either previously known to cause diseases in salmon or assumed to be associated with salmon diseases worldwide (Miller et al, ).…”

Section: Methodsmentioning

confidence: 99%

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985–94)

Thakur

Vanderstichel

Kaukinen

et al. 2019

Journal of Fish Diseases

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In response to concerns that novel infectious agents were introduced through the movement of eggs as Atlantic salmon aquaculture developed in British Columbia (BC), Canada, we estimated the prevalence of infectious agents in archived return‐migrating Sockeye salmon, from before and during aquaculture expansion in BC (1985–94). Of 45 infectious agents assessed through molecular assays in 652 samples, 23 (7 bacterial, 2 viral and 14 parasitic) were detected in liver tissue from six regions in BC. Prevalence ranged from 0.005 to 0.83 and varied significantly by region and year. Agent diversity ranged from 0 to 12 per fish (median 4), with the lowest diversity observed in fish from the Trans‐Boundary and Central Coast regions. Agents known to be endemic in Sockeye salmon in BC, including Flavobacterium psychrophilum, Infectious haematopoietic necrosis virus, Ceratonova shasta and Parvicapsula minibicornis, were commonly observed. Others, such as Kudoa thyrsites and Piscirikettsia salmonis, were also detected. Surprisingly, infectious agents described only recently in BC salmon, Ca. Branchiomonas cysticola, Parvicapsula pseudobranchicola and Paranucleospora theridion, were also detected, indicating their potential presence prior to the expansion of the aquaculture industry. In general, our data suggest that agent distributions may not have substantially changed because of the salmon aquaculture industry.

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Section: Methodsmentioning

confidence: 99%

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985–94)

Thakur

Vanderstichel

Kaukinen

et al. 2019

Journal of Fish Diseases

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“…Gene expression profiles consistent with an immune response to viruses have been associated with mortality in wild migratory smolts and adults (28,29), as well as in unexplained aquaculture mortalities of salmon in marine net pens in BC (30,31). Together, these suggest there are a range of viruses that may 80 contribute to decreased survival of migratory salmon in BC.…”

Section: Introductionmentioning

confidence: 90%

“…The VDD panel of host transcriptional biomarkers is capable of differentiating fish in an active RNA viral disease state from those carrying bacterial or fungal disease (30). For sequencing, we selected farmed Atlantic and farmed Chinook salmon which exhibited a strong viral disease development (VDD) signal, but were negative for any RNA viruses known to infect salmon in the North Pacific.…”

Section: Viral Disease Development (Vdd) Biomarkers and Virus Discoverymentioning

confidence: 99%

“…Studying disease in wild populations is exceedingly complex (34), and although terrestrial strategies can include treating for known infectious agents, fish health investigations often begin with discovery. In the ocean, mortality events are rarely observed; our sampling efforts solely capture live fish, and weak and dying fish are probably predated before the disease progresses to mortality (27,30). In order to surmount some of these difficulties, and to select samples for virus discovery, we applied a viral disease 90 development (VDD) biomarker panel shown to be predictive of an active RNA virus infection in salmon (30) followed by metatranscriptomic sequencing, molecular surveillance and in-situ hybridisation to prove infection.…”

mentioning

confidence: 99%

“…In the future, the VDD panel will be an important tool to enable the discovery of viruses in wild salmon, in which we expect to find fewer positive or high-load samples than in farmed fish. Moreover, given the high overlap in genes contributing to the salmon VDD panel and those discovered to be predictive of respiratory viral diseases in humans (83,84), there is a high potential 380 that a similar panel of genes could be applied for viral discovery in a diverse range of vertebrate host species (30).…”

mentioning

confidence: 99%

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Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing

Mordecai¹,

Cicco²,

Günther³

et al. 2020

Preprint

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The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance and epidemiology of aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers to identify and select fish 25 in a viral disease state but only those that we also showed to be negative for established viruses. This was followed by metatranscriptomic sequencing to determine the viromes of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia. We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered viruses that have not previously been characterized in British Columbian 30 Atlantic salmon farms. To determine the epidemiology of the newly discovered or emerging viruses we conducted high-throughput RT-PCR to reveal their prevalence in British Columbia (BC), and detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook and sockeye salmon, suggesting a broad host range. Finally, we applied in-situ hybridisation to confirm infection and explore the tissue tropism of each virus. 35

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A Comparison of Nonlethal and Destructive Methods for Broad‐Based Infectious Agent Screening of Chinook Salmon Using High‐Throughput qPCR

Teffer

Miller

2019

J Aqua Anim Hlth

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Molecular tools, such as high-throughput quantitative polymerase chain reaction (HT-qPCR), are useful for monitoring multiple infectious agents in wild animal populations (i.e., broad-based screening). If destructive tissue samples cannot be obtained due to experimental design requirements (e.g., bio-telemetry; holding with repeated biopsy) or the conservation status of host species, then nonlethally sampled tissues can be substituted. However, infection profiles have been found to differ between nonlethally and destructively sampled tissues. We present a comparative analysis of nonlethal (gill and blood) and destructive (pool of internal and external tissue) approaches for broad-based infectious agent screening of adult Chinook Salmon Oncorhynchus tshawytscha. Of a possible 47 agents, 16 were detected overall by nonlethal and destructive methods. Our results indicated moderate differences in infection profiles among tissues, with limitations of each tissue type dependent on the ecology of each agent. The gill was the most comprehensive screening tissue, as more infectious agents were detected overall in gill (n = 16) than in blood (n = 12) or multi-tissue pools (n = 15). The agreement in the estimated agent prevalence between tissue types ranged from poor to excellent, while overall agent community structure (the combined prevalence of all agents) showed low agreement between tissue types. Two agents occurred at 100% prevalence in all tissue types. Nine agents, including types of bacteria and gill parasites, were more prevalent in gill than in blood, while five agents, including one virus and several microparasites, were more prevalent in blood. Future studies should pair microscopy and histopathology with HT-qPCR to better characterize host health and disease development relative to molecular detection of agents across tissue types.

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Molecular indices of viral disease development in wild migrating salmon†

Cited by 76 publications

References 72 publications

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985–94)

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985–94)

Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing

A Comparison of Nonlethal and Destructive Methods for Broad‐Based Infectious Agent Screening of Chinook Salmon Using High‐Throughput qPCR

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