Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR

Abstract

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 in a viral disease state, but only those that were negative for known viruses based on RT-PCR screening. These fish were selected for metatranscriptomic sequencing to discover potential viral pathogens of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia (BC). We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered two viruses that have not previously been characterized in Atlantic salmon farms in BC (Atlantic salmon calicivirus and Cutthroat trout virus-2), as well as partially sequenced three putative novel viruses. To determine the epidemiology of the newly discovered or emerging viruses we conducted high-throughput RT-PCR and screened over 9000 farmed and wild salmon sampled over one decade. Atlantic salmon calicivirus and Cutthroat trout virus-2 were in more than half of the farmed Atlantic salmon we tested. Importantly we detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook salmon, suggesting a broad host range. Finally, we applied in-situ hybridisation to determine infection and found differing cell tropism for each virus tested. Our study demonstrates that continual discovery and surveillance of emerging viruses in these ecologically important salmon will be vital for management of both aquaculture and wild resources in the future.

Infected juvenile salmon can experience increased predation during freshwater migration

“…Moreover, as demonstrated in human diagnostic studies, the molecular panel could identify disease before clinical or morphological evidence can be observed [ 32 , 33 ], and due to the systemic nature of viral infections, worked well across a range of tissues. The VDD technology has been successfully applied to study disease development pathways for Piscine orthoreovirus (PRv) [ 33 ] and has led to the discovery of over a dozen novel viruses in salmon [ 34 , 35 ].…”

Distribution and Pathogenicity of Two Cutthroat Trout Virus (CTV) Genotypes in Canada

“…Additionally, a PSAP motif, conserved across ORF3 proteins of all known HEV strains, including avian HEV, appears necessary for the formation of membrane-associated HEV particles [30][31][32][33]. The involvement of ORF3 in the egress of particles is interesting to consider in the context of CTV-2, as the particular isolate evaluated in our study appears to be lacking a putative homolog of ORF3 which was previously reported for a CTV-2 isolate from BC [10]. A PTAP motif (Table S6), along with a prominent serine rich region (22-28 amino acids; Figure S4), was identified within the non-structural polyprotein of the Canadian Piscihepeviruses; however, it is unknown whether these sites have any functional involvement in the release of virus.…”

Innate antiviral defense demonstrates high energetic efficiency in a bony fish

“…We interpret our results as indicating that the ancestral vertebrate autocrine and paracrine "antiviral state" created in localized tissues and cells as a result of interferon activation appears to be within the short-term allostatic capacity of the organism to maintain homeostasis and thus does not imply a life-history tradeoff in terms of aerobic or anaerobic performance. This is an important consideration in the current age of viral discovery and host transcriptional monitoring, given that viral recognition by the host has repeatedly been interpreted as an implicit sign of disease and/or harm [52][53][54]. Our work indicates that if a life-history tradeoff is not inherently implied via activation of the interferon system, then components of this system cannot be inferred to imply a viral-associated disease state or functional harm to the organism.…”