Abstract
The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture.
Highlights
Pacific salmon (Oncorhynchus spp.) species have supported coastal ecosystems and Indigenous populations surrounding the North Pacific Ocean for tens of millennia
Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations
Fish were screened against a viral disease detection biomarker panel (VDD) that elucidates a conserved transcriptional pattern indicative of an immune response to active RNA viral infection (Miller et al, 2017)
Summary
Pacific salmon (Oncorhynchus spp.) species have supported coastal ecosystems and Indigenous populations surrounding the North Pacific Ocean for tens of millennia. While farmed Pacific salmon may pose some transmission risk to their wild counterparts, they offer the opportunity to study disease processes that are not readily observable in wild salmon Such data can be used to develop policies to minimize the impact of these infectious agents and improve the survival of wild salmon populations. Immune responses to viruses such as Infectious haematopoietic necrosis virus (IHNV) and potentially undiscovered viruses, have been associated with mortality in wild juvenile salmon (Jeffries et al, 2014). This is an important observation as mortality of juvenile salmon can be as high as ~90% transitioning from fresh water to the marine environment (Clark et al, 2016). Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations
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