Detection and phylogenetic assessment of PRV-1 via sampling of biological materials released from salmon farms in British Columbia

Abstract

The growth of the net pen salmon farming industry and the concurrent decline of many wild salmon populations have generated an ongoing call for research into the potential role of infectious agents associated with salmon farming. Here, we describe a method to screen for the presence of viral nucleic acids by sampling biological waste in the vicinity of farms. We collected biological samples adjacent to 56 marine net pens from five different companies, and two farm salmon processing plants ( n = 230), 70% of samples were positive for Piscine orthoreovirus-1 (PRV-1). Viral genome segments S1 ( n = 68) and M2 ( n = 39) were sequenced and subjected to phylogenetic analysis. Sequences were all monophyletic to the clade of PRV-1 routinely found in the region. Consistent with previous studies, samples collected near Atlantic salmon ( Salmo salar) farms were related to a lineage of PRV-1a commonly detected in both farmed and wild salmon in British Columbia, while a related lineage of PRV-1a was detected near Chinook salmon ( Oncorhynchus tshawytscha) farms. Similarity in sequence within companies suggests that Atlantic salmon freshwater hatcheries are a probable source of this virus to the marine environment, concordant with recent detections of PRV-1 within those hatcheries.