Disease and Health

This project will address whether the disappearance of juvenile Chinook and coho salmon (hatchery and wild) at sea between May and September is a result of disease and/or condition of fish upon entry into the ocean.  It involves three projects assessing the health and fitness of hatchery and wild coho salmon using state-of-the-art ecological genomic methods, assessments of natural pathogens, and controlled rearing studies.
gene array
A gene array slide used in genomics research.  One gene array can assess at once the expression of all genes in an individual’s genome. Currently, salmon arrays contain 44,000 gene transcripts.

Since the 2009 proposal, a major research initiative concerning the presence and distribution of salmon microbes in BC Pacific salmon.  This research supported by Genome BC, DFO (Dr. Kristi Miller-Saunders), and the Pacific Salmon Foundation (Dr. B. Riddell) is investigating the possible presence of 47 known microbes of salmon, including all species of wild salmon, hatchery reared salmon, and aquaculture-raised (sea pens) Atlantic salmon.

Team: Kristi Miller-Saunders (DFO-PBS), Karia Kaukinen (DFO-PBS), Amy Tabata (DFO-PBS)

The main objective of the Strategic Salmon Health Initiative (SSHI) is to determine what pathogens/diseases, if any, may be undermining the productivity and performance of BC salmon, their evolutionary history, and the potential role of exchanges between wild and cultured salmon.

Samples collected from the juvenile sampling study (described above) are used for a variety of physiological and genomic studies, involving a number of researchers from UVic and DFO.

Researchers are using novel genomic approaches that utilize the activity of the genes to conduct physiological assessments to identify potential stressors and diseases impacting salmon and apply quantitative assays to monitor dozens of infectious agents to identify viruses, bacteria and microparasites undermining salmon health and survival. The sampling program utilizes a trajectory from freshwater through the first 9 months of marine residence, and thus the conditional state of fish can be monitored even before they enter the Salish Sea. Prior analyses have suggested that salmon pre-condition can be highly predictive of survival as they move into new stressful environments.

In the previous phase of the project, the team developed and analytically validated a high throughput molecular-based infectious agent monitoring platform to detect and quantitative 46 pathogens known or suspected to cause disease in salmon world-wide simultaneously in 96 fish. This platform is being applied to over 26,000 wild, enhancement hatchery and aquaculture salmon in the current phase of the project (2b) to discover the microbes present in BC salmon and their spatial and temporal distributions within and among species and cultured and wild stocks. Multiple metrics to assess physiological and organismal impacts are being merged with the microbe data to discern the pathogenic potential of each microbe.


  • The SSHI project specifically addressed the hypothesis that infectious disease is impacting early marine survival of salmon in the Salish Sea. The project also addresses the potential that salmon aquaculture interactions may contribute to risk of disease in Pacific salmon smolts.  The project has identified a number of infectious agents that are showing strong pathogenic potential in the Salish sea environment, most notably parasites Pavicapsula minibicornis, Ceratonova shasta, Loma, Paranucleospora theridion, and Tetracapsuloides bryosalmonae, and viruses PRV and ENV.  Moreover, two different strains of a novel arenavirus have been shown to infect Chinook and Sockeye salmon in the Salish sea, and their potential linkages with disease is currently under study.  Their sockeye smolt tracking studies have identified linkage between IHNV and migratory survival in the river, but it appears that predators, specifically Bull Trout, largely consume infected fish before the reach the Salish Sea.  Hence, their research is also demonstrating linkages between infection status and risk of predation, and the potential role that predators may play in removing infected individuals and thereby increasing the general health of the populations.  Given the strong evidence that seals may be consuming large numbers of smolts, it would be highly useful to determine if infection status could pose an enhanced risk of predation.
  • Their SSHI project (phase 2b) is a three year project and they are well on track with meeting their objectives. They are now focusing in on agents with highest pathogenic potential and gathering the evidence to support their potential for impact.  They are also running smolt samples collected over a decade and will assess whether any agents, or combinations of agents are associated with year-class strength, stock-specific marine survival estimates, and life-history variation (subyearlings are faring better than yearling Chinook).  For the latter question, they have already shown that the agents of most concern are found at higher prevalence and show stronger levels of seasonal truncation in yearling Chinook, potentially contributing to their poor performance.
  • They are on track, and have exceeded their expectations in terms of the development of novel approaches and technologies to study disease impacts in wild salmon. The molecular viral disease diagnostic tool and the in situ hybridization tool (specifically developed by PSF fellow Emiliano Di Cicco) were not anticipated at project start but have greatly enhanced their ability to move from agent to disease characterization.
  • This project will contribute to their understanding of the role of infectious disease in early marine survival of salmon, but is also contributing to ongoing risk assessments associated with the salmon aquaculture industry.