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 were negative for known viruses based on RT-PCR screening. These fish were selected for metatranscriptomic sequencing to discover potential viral pathogens of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia (BC). We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered two viruses that have not previously been characterised in Atlantic salmon farms in BC (Atlantic salmon calicivirus and Cutthroat trout virus-2), as well as partially sequenced three putative novel viruses. To determine the epidemiology of the newly discovered or emerging viruses, we conducted high-throughput reverse transcription polymerase chain reaction (RT-PCR) and screened over 9,000 farmed and wild salmon sampled over one decade. Atlantic salmon calicivirus and Cutthroat trout virus-2 were in more than half of the farmed Atlantic salmon we tested. Importantly we detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook salmon, suggesting a broad host range. Finally, we applied in situ hybridisation to determine infection and found differing cell tropism for each virus tested. Our study demonstrates that continual discovery and surveillance of emerging viruses in these ecologically important salmon will be vital for management of both aquaculture and wild resources in the future.

中文翻译：

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使用病毒免疫反应生物标记，元转录组学和高通量RT-PCR发现和监测不列颠哥伦比亚省鲑鱼的病毒

传染源的出现给水产养殖生产带来了持续的经济和环境挑战，但水生病毒的多样性，丰度和流行病学特征不佳。在这项研究中，我们应用了鲑鱼宿主转录生物标记物来识别和选择处于病毒性疾病状态的鱼类，但仅基于RT-PCR筛选对已知病毒呈阴性的鱼类。选择这些鱼进行转录组测序，以发现死亡和垂死的大西洋养殖（Salmo salar）和奇努克（Chinook）（Oncorhynchus tshawytscha）的潜在病毒病原体。）不列颠哥伦比亚省（BC）的鲑鱼。我们发现生物标志物组的应用增加了在水产养殖种群中发现病毒的可能性。我们发现了不列颠哥伦比亚省的大西洋鲑鱼养殖场以前未鉴定出的两种病毒（大西洋鲑鱼杯状病毒和Cutthroat鳟鱼病毒2），以及对三种推定的新型病毒进行了部分测序。为了确定新发现或新兴病毒的流行病学，我们进行了高通量逆转录聚合酶链反应（RT-PCR），并在十年内筛选了9000多种养殖鲑鱼和野生鲑鱼。在我们测试的养殖大西洋鲑鱼中，大西洋鲑鱼杯状杯状病毒和残酷鳟鱼病毒2占一半以上。重要的是，我们检测到了我们首先在奇努克鲑鱼养殖的大西洋鲑鱼中发现的一些病毒，建议主机范围广泛。最后，我们申请了原位杂交以确定感染，并发现每种测试病毒的细胞嗜性不同。我们的研究表明，在这些对生态具有重要意义的鲑鱼中，不断发现和监测新兴病毒对于将来管理水产养殖和野生资源至关重要。