Mordecai Gideon J, Di Cicco Emiliano, Günther Oliver P, Schulze Angela D, Kaukinen Karia H, Li Shaorong, Tabata Amy, Ming Tobi J, Ferguson Hugh W, Suttle Curtis A, Miller Kristina M
Department of Medicine, University of British Columbia, 2775 Laurel Street, 10th Floor Vancouver, BC Canada V5Z 1M9, Canada.
Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada.
Virus Evol. 2020 Sep 1;7(1):veaa069. doi: 10.1093/ve/veaa069. eCollection 2021 Jan.
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 () and Chinook () 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 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.
感染源的出现对水产养殖生产构成了持续的经济和环境挑战，然而水生病毒的多样性、丰度和流行病学特征却鲜为人知。在本研究中，我们应用鲑鱼宿主转录生物标志物来识别和挑选处于病毒感染状态的鱼类，但仅限于那些基于逆转录聚合酶链反应（RT-PCR）筛选对已知病毒呈阴性的鱼。挑选这些鱼进行宏转录组测序，以发现不列颠哥伦比亚省（BC）养殖的死亡和濒死大西洋鲑鱼（）和奇努克鲑鱼（）的潜在病毒病原体。我们发现，生物标志物组的应用增加了在养殖群体中发现病毒的可能性。我们发现了两种此前在BC省大西洋鲑鱼养殖场未被鉴定的病毒（大西洋鲑杯状病毒和溪鳟病毒-2），并对三种假定的新型病毒进行了部分测序。为了确定新发现或新出现病毒的流行病学特征，我们进行了高通量逆转录聚合酶链反应（RT-PCR），并对十多年来采集的9000多条养殖和野生鲑鱼进行了筛选。在我们检测的一半以上养殖大西洋鲑鱼中发现了大西洋鲑杯状病毒和溪鳟病毒-2。重要的是，我们在奇努克鲑鱼中检测到了一些我们最初在养殖大西洋鲑鱼中发现的病毒，这表明这些病毒具有广泛的宿主范围。最后，我们应用杂交技术来确定感染情况，并发现每种测试病毒具有不同的细胞嗜性。我们的研究表明，持续发现和监测这些具有生态重要性的鲑鱼中出现的病毒，对于未来水产养殖和野生资源的管理至关重要。
