Abstract Emerging diseases are impacting animals under high‐density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity populations, as once the host dies, there limited opportunities infect new individuals. Instead, moderately virulent microparasites persisting long periods across multiple environments of greatest concern. Evolved resistance endemic may...

The collapse of iconic, keystone populations sockeye (Oncorhynchus nerka) and Chinook tshawytscha) salmon in the Northeast Pacific is great concern. It thought that infectious disease may contribute to declines, but little known about viruses endemic salmon. Metatranscriptomic sequencing surveillance dead moribund cultured revealed a novel arenavirus, reovirus nidovirus. Sequencing two different arenavirus variants which each infect wild In situ hybridisation localised mostly blood cells....

Abstract The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging the Columbia River to Japan. For loci, number of alleles observed a related power in providing accurate estimates stock composition single‐population mixtures. In an analysis mixtures where Pacific Rim baseline used estimation identification, 80% accuracy average population achieved by...

Piscine orthoreovirus Strain PRV-1 is the causative agent of heart and skeletal muscle inflammation (HSMI) in Atlantic salmon (Salmo salar). Given its high prevalence net pen salmon, debate has arisen on whether PRV poses a risk to migratory especially British Columbia (BC) where commercially important wild Pacific are decline. Various strains have been associated with diseases including erythrocytic inclusion body syndrome (EIBS), HSMI-like disease, jaundice/anemia Japan, Norway, Chile...

Molecular epidemiology reveals that aquaculture contributes to emergence of a fish virus at both global and local epidemic hierarchies.

The utility of DNA-based variation for stock identification was evaluated Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the at 14 microsatellite loci and one major histocompatibility complex (MHC) locus determined from approximately 13,000 fish 47 populations in drainage. Genetic differentiation among observed, overall FST value surveyed being 0.054 that MHC 0.215. regions within 20 times as great annual 28 locus. power a population-specific simulated mixture samples...

The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk management concern salmon aquaculture fisheries. Using quantitative environmental DNA methodology, we assessed pathogen in relation to farms coastal British Columbia, Canada, by testing 39 species pathogens (viral, bacterial, eukaryotic) 134 marine samples at 58 farm sites (both active inactive) over 3 years. Environmental 22 was detected 496 times varied their occurrence...

Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At same time many Pacific salmon populations declined abundance as result reduced survival. However, few studies explicitly considered potential pathogens could these declines. Using multi-year dataset spanning 59 pathogen taxa Chinook and Coho sampled along British Columbia coast, we carried out exploratory analysis to quantify evidence...

Infectious diseases may contribute to declines in Fraser River Sockeye salmon (Oncorhynchus nerka) stocks, but a clear knowledge gap exists around which infectious agents and are important. This study was conducted to: 1) determine the presence prevalence of 46 juvenile salmon, 2) evaluate spatial patterns burden over initial seaward migration, contrasting between two years average poor productivity. In total, 2,006 out-migrating were collected from four regions along their migration...

Abstract The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance, epidemiology aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers identify select fish in viral disease state, but only those that were negative for known based on RT-PCR screening. These selected metatranscriptomic sequencing discover potential pathogens dead dying farmed Atlantic...

Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), metabarcoding with multiple markers (i.e., 16S, 18S-dinoflagellate 18S-diatom, large subunit (28S) rDNA) were applied on samples ( n = 54) containing suspected algae (e.g., Alexandrium...

Salmon are keystone species across the North Pacific, supporting ecosystems, commercial opportunities, and cultural identity. Nevertheless, many wild salmon stocks have experienced significant declines. restoration efforts focus on fresh coastal waters, but little is known about open ocean environment. Here we use high throughput RT-qPCR tools to provide first report health, condition, infection profile of coho, chum, pink, sockeye in Gulf Alaska during 2019 winter. We found lower infectious...

Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from arises, differential patterns live dead fish difficult collect wild populations, potential risks associated with agent transmission between farmed hosts. We report results a multi-year infectious-agent screening program British Columbia, Canada, using...

ABSTRACT Marine biodiversity worldwide is rapidly declining, and nowhere this more evident than in coastal ecosystems where the impacts of climate change anthropogenic activities concentrate. The ongoing crisis affects all components marine food web, but data required to monitor shifts at continental scales are scarce taxonomically spatially heterogeneous. application environmental DNA metabarcoding can complement traditional approaches monitoring biodiversity, its efficiency detecting...

Infectious diseases are likely contributing to large-scale declines in chinook salmon stocks the Pacific Northwest, but specific agents and involved, prevalences migratory salmon, mostly unknown. We applied a high-throughput microfluidics platform screen for 45 infectious 556 out-migrating juvenile collected from freshwater (FW) saltwater (SW) locations Cowichan River system on Vancouver Island, Canada, during 2014. Nineteen (5 bacterial, 2 viral, 12 parasitic) were detected, with ranging...

Infectious agents are key components of animal ecology and drivers host population dynamics. Knowledge their diversity transmission in the wild is necessary for management conservation species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout life cycle, evidence lacking to support during mixing at sea or between farmed due aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious potential among sub-adult marine...

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides suite genes to examine role genetic diversity at non-neutral loci for population persistence. We contrasted patterns two classical MHC in sockeye salmon (Oncorhynchus nerka), class I (UBA) and II (DAB), neutral microsatellite across 70 populations spanning species range from Washington State Japan. There was no correlation allelic richness or heterozygosity between microsatellites....

Viral erythrocytic necrosis (VEN) affects over 20 species of marine and anadromous fishes in the North Atlantic Pacific Oceans. However, distribution strain variation its viral causative agent, virus (ENV), has not been well characterized within salmon. Here, metatranscriptomic sequencing Chinook salmon revealed that ENV infecting was closely related to from herring, with inferred amino-acid sequences being 99% identical those reported for herring. Sequence analysis also 89 protein-encoding...

Abstract The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance epidemiology aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers identify select fish in viral disease state but only those that also showed be negative for established viruses. This was followed by metatranscriptomic sequencing determine viromes dead dying farmed Atlantic ( Salmo...

Abstract The variation at 14 microsatellite loci and 1 major histocompatibility complex locus was surveyed in 12,000 sockeye salmon Oncorhynchus nerka from 35 populations the Skeena Nass River drainages British Columbia 20 Southeast Alaska. Genetic differentiation among observed, with an overall F ST of 0.104. Evaluation utility for stock identification applications indicated that accuracy precision estimated compositions generally increased as number observed alleles increased. Analysis...

Abstract Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), metabarcoding with multiple markers ( i.e. 16S, 18S-dinoflagellate 18S-diatom, large subunit (28S) rDNA) were applied on samples (n=54) containing suspected algae (e.g....