ABSTRACT: Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

中文翻译：

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纳米孔全基因组测序和分区系统发育分析支持新的鲑鱼甲病毒基因型（SAV7）

摘要：鲑鱼胰腺疾病病毒沙门氏菌，更通常称为鲑鱼甲病毒（SAV），是一种单链正向RNA病毒，是鲑鱼胰腺疾病和睡眠疾病的病原体。在这项研究中，以前从Ballan濑鱼中分离出的SAV独特株系经过了纳米孔测序的全基因组测序。为了与其他SAV菌株相比准确地检查该菌株的进化史，进行了分区系统发育分析，以说明单个基因和密码子位置的进化速率变化。与在基因组中应用一种替代模型的更常见方法相比，对基因组对齐进行分区的方法几乎使在系统发生树中观察到的分支长度增加了一倍，并且显着提高了最适合核苷酸替代模型的统计拟合度。根据基因组数据，可以为本研究中检测到的病毒株做出新的SAV基因型提供有效案例。此外，这项研究增加了越来越多的研究，其中发现SAV会感染非鲑鱼，因此，我们建议将病毒种类名称修改为更具包容性的“鱼甲病毒”。