Abstract Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I–IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) ‘Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon’, PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.

中文翻译：

---

基因组揭示了来自加拿大和美国的养殖和自由放养鲑鱼中鱼正肠病毒的遗传多样性

摘要 Piscine orthoreovirus (PRV-1) 是一种分段RNA 病毒，常见于大西洋和太平洋的鲑鱼中。PRV-1 导致大西洋鲑鱼的心脏和骨骼肌炎症疾病，并与其他几种疾病有关。先前对基因组片段 1 (S1) 的系统发育研究确定了 PRV-1 的四个主要基因组（S1 基因组 I-IV）。本研究的目标是使用贝叶斯系统发育推断来扩大我们对来自东北太平洋水域的 PRV-1 的空间、时间和宿主模式的理解。为此，我们确定了 14 个 PRV-1 样本的编码基因组序列，这些样本是为了提高我们对更广泛的时间、地理和宿主范围内的遗传多样性的了解，包括来自西北大西洋（加拿大东部）的首次报道的基因组序列。串联基因组及其各个片段的核苷酸和氨基酸序列表明，在所有分析中，来自东北太平洋的已建立序列都是单系的。使用 BEAST 和 MrBayes 的 S1 序列的贝叶斯推断系统发育树还发现，来自东北太平洋的序列与来自其他地区的序列分开分组。一个来自逃逸大西洋鲑鱼的 PRV-1 样本 (WCAN_BC17_AS_2017)，收集于不列颠哥伦比亚省，但来自冰岛亲鱼，与来自冰岛的其他 S1 序列分组。我们的串联基因组和 S1 分析表明，来自东北太平洋的 PRV-1 在遗传上是不同的，但它是来自北大西洋的 PRV-1 的后裔。然而，这些分析对于从北美东部或北大西洋的欧洲水域引入东北太平洋的时间和确切来源尚无定论。没有证据表明 PRV-1 在自由放养的太平洋鲑鱼和养殖的大西洋鲑鱼之间进化不同。根据 Garseth、Ekrem 和 Biering 的分类，东北太平洋 PRV-1 序列属于基因组 II（Garseth, AH、Ekrem, T. 和 Biering, E. (2013) 'Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon', PLoS One, 8: e82202.)，其中还包括来自加拿大东部、冰岛和挪威的北大西洋序列。