A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks

Abstract

Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to support transmission during population mixing at sea or between farmed and wild salmon due to aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious agents and transmission potential among sub-adult Atlantic salmon at marine feeding areas and adults in three eastern Canadian rivers with varying aquaculture influence. We used high-throughput qPCR to quantify infection profiles and next generation sequencing to measure genomic variation among viral isolates. We identified 14 agents, including five not yet described as occurring in Eastern Canada. Phylogenetic analysis of piscine orthoreovirus showed homology between isolates from European and North American origin fish at sea, supporting the hypothesis of intercontinental transmission. We found no evidence to support aquaculture influence on wild adult infections, which varied relative to environmental conditions, life stage, and host origin. Our findings identify research opportunities regarding pathogen transmission and biological significance for wild Atlantic salmon populations.

Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR

“…2008 ), so it is not surprising that they are found extensively in all groups of vertebrates and cause a wide variety of diseases in mammals and birds ( Wolf et al. 2009 ; Tse et al. 2012 ; Scheuer et al.…”

Piscine orthoreovirus: Biology and distribution in farmed and wild fish

“…PRV prevalence in wild Atlantic Salmon of Eastern North American is limited. In a recent study, PRV was not detected in 60 returning wild Atlantics salmon screened in New Brunswick, suggesting that prevalence would be 5% or less in that cohort (Teffer et al., 2020). In contrast, multiple molecular screening studies of wild‐caught Pacific salmon and trout from western North America involving almost 13,000 specimens have demonstrated that PRV‐1 detection can vary dramatically between species and stocks in this region.…”

“…Retrospective screening of eight Atlantic Salmon diagnosed with haemorrhagic kidney syndrome from two farmed populations in New Brunswick in 1996 was all shown to be positive for PRV nucleic acid and protein (Ferguson et al., 2020). More recently, PRV has been detected in escaped farmed Atlantic Salmon (Teffer et al., 2020) and in most other instances where net‐pen farmed Atlantic Salmon have been screened (N. Gagne, personal communication), suggesting that PRV‐1 is likely ubiquitous in farmed Atlantic Salmon in the region and has been so for at least the last few decades.…”

“…Nevertheless, comparisons of PRV prevalence in wild adult salmon from regions of northern Norway with differing farming intensity and disease frequency showed no association between salmon farming and the prevalence of PRV infection in wild salmon (Madhun et al., 2018). Similarly, in eastern Canada, no effect of aquaculture proximity on PRV infection was observed in returning wild Atlantic Salmon from two river systems (Teffer et al., 2020). To date, HSMI has not been documented in any wild or escaped salmon in Europe or North America.…”

“…PRV‐1 has also been detected in farmed Atlantic Salmon from Eastern Canada (Ferguson et al., 2020; Siah et al, in press ; Teffer et al., 2020). Retrospective screening of eight Atlantic Salmon diagnosed with haemorrhagic kidney syndrome from two farmed populations in New Brunswick in 1996 was all shown to be positive for PRV nucleic acid and protein (Ferguson et al., 2020).…”