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Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing

View ORCID ProfileGideon J. Mordecai, View ORCID ProfileEmiliano Di Cicco, View ORCID ProfileOliver P. Günther, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Tobi J. Ming, Hugh W. Ferguson, View ORCID ProfileCurtis A. Suttle, Kristina M. Miller
doi: https://doi.org/10.1101/2020.02.13.948026
Gideon J. Mordecai
1Department of Medicine, University of British Columbia, Vancouver, Canada
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  • For correspondence: gidmord@gmail.com
Emiliano Di Cicco
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
3Pacific Salmon Foundation, Vancouver, Canada
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Oliver P. Günther
4Günther Analytics, Vancouver, Canada
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Angela D. Schulze
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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Karia H. Kaukinen
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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Shaorong Li
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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Amy Tabata
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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Tobi J. Ming
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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Hugh W. Ferguson
5School of Veterinary Medicine, St. George’s University, True Blue, Grenada
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Curtis A. Suttle
6Department of Botany, University of British Columbia, Vancouver, Canada
7Institute for the Oceans and Fisheries. University of British Columbia, Vancouver, Canada
8Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
9Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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Kristina M. Miller
2Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
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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 we also showed to be negative for established viruses. This was followed by metatranscriptomic sequencing to determine the viromes of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia. We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered viruses that have not previously been characterized in British Columbian Atlantic salmon farms. To determine the epidemiology of the newly discovered or emerging viruses we conducted high-throughput RT-PCR to reveal their prevalence in British Columbia (BC), and detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook and sockeye salmon, suggesting a broad host range. Finally, we applied in-situ hybridisation to confirm infection and explore the tissue tropism of each virus.

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Posted February 13, 2020.
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Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing
Gideon J. Mordecai, Emiliano Di Cicco, Oliver P. Günther, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Tobi J. Ming, Hugh W. Ferguson, Curtis A. Suttle, Kristina M. Miller
bioRxiv 2020.02.13.948026; doi: https://doi.org/10.1101/2020.02.13.948026
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Emerging viruses in British Columbia salmon discovered via a viral immune response biomarker panel and metatranscriptomic sequencing
Gideon J. Mordecai, Emiliano Di Cicco, Oliver P. Günther, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Tobi J. Ming, Hugh W. Ferguson, Curtis A. Suttle, Kristina M. Miller
bioRxiv 2020.02.13.948026; doi: https://doi.org/10.1101/2020.02.13.948026

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