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)

Objective:
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.

Background:
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.

Status:
Phase 2b funding from Genome BC was signed off in April 2016, and research has progressed quickly. In May, the SSHI team announced the novel finding of Heart and Skeletal Muscle Inflammatory (HSMI) disease on one of the four salmon farms that were sampled over the entire ocean production cycle by the SSHI researchers. While the disease was diagnosed using the world-recognized pathological standard of inflammatory lesions in heart and skeletal muscle tissue, the researchers were also able to show that, as in other parts of the world, piscine orthoreovirus (PRV) was associated with the disease both statistically and through its distribution within the tissues and infected cells, and that clinical signs of the disease were also present. A manuscript on this finding, led by PSF-supported veterinary pathologist Emiliano Di Cicco, is now in the final stages of review for publication. PRV has been the subject of an ongoing court case, and these data are now being carefully examined by policy makers within DFO.

The SSHI team obtained 900 samples of farmed salmon through the DFO Audit program, and has completed the infectious agent monitoring and histopathology data collection on these fish; these data are now being analyzed by Postdoctoral fellows (supported by PSF and MITACS) conducting epidemiological research at University of Prince Edward Island (UPEI) to identify linkages between infectious agents and pathology on farms. One finding of note is a higher incident and diversity of infectious agents observed in farmed Chinook versus farmed Atlantic salmon.

A smolt out-migration study was undertaken encompassing infectious agent monitoring of >1,800 Chinook Salmon and is presently being analyzed and incorporated into a manuscript. The manuscript will describe potential pathogens infecting outmigrating Fraser River Chinook smolts emanating from freshwater hatcheries and transmitted in the early marine environment (first 9 months) and will show that half of the 32 microbes detected originated in freshwater. Moreover the study identifies a half dozen microbes that show seasonal shifts in prevalence and load in the ocean consistent with the potential for impact on the migratory salmon.

A study linking acoustic tracking and microbe and host transcription profiling funded through NSERC co-funding found that Sockeye smolts with enhanced anti-viral immune activation and infection with the IHN virus suffered high migratory failure during early down-stream migration (Jeffries et al. 2014). A follow-up study was undertaken and showed that fish carrying the IHN virus were 34 times more likely to be eaten by resident bull trout in the clear waters of the Chilcotin River, which may explain the early high losses associated with this virus; this work is part of a PhD thesis being defended in July 2016. A similar study on predation by Rhinoceros Auklets also carried out by the team also showed that infection status was associated with increased risk of predation. Together, these data suggest that 1) predators may increase the overall health of salmon populations by removing infected individuals and reducing risk of transmission, 2) sub-lethal impacts of infection that impact salmon performance (e.g. swimming, schooling, behavior, visual acuity, etc) likely puts them at greater risk of predation, perhaps even during early stages of disease development, and 3) if predators preferentially remove infected individuals, it will be quite rare to sample migratory fish in a late-stage of disease, making it very difficult to utilize classical diagnostic approaches to understand disease impacts on wild fish.

With co-funding from the DFO Genomic Research and Development Initiative, the SSHI team has added to their arsenal of host biomarkers a panel of genes that together can predict the development of a viral disease (VDD) state and can distinguish fish that are latent carriers of salmon viruses from those that are undergoing active, disease causing infections. This VDD panel has been validated to work across multiple viral species, salmon species, and salmon tissues, and can even predict the presence of a systemic viral disease state based on sampling of non-destructive gill tissue. Moreover, it works in the presence of numerous co-infecting organisms and can distinguish viral from bacterial infections. This disruptive technology moves the molecular monitoring program of the SSHI from pathogen detection to disease detection and will be expanded to recognize bacterial disease states and those brought on by different classes of microparasites.