Tighe Andrew J, Gallagher Michael D, Carlsson Jens, Matejusova Iveta, Swords Fiona, Macqueen Daniel J, Ruane Neil M
Fish Health Unit, Marine Institute, Oranmore H91 R673, Ireland.
Dis Aquat Organ. 2020 Dec 17;142:203-211. doi: 10.3354/dao03546.
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'.
鲑鱼胰腺疾病病毒，通常更被称为鲑鱼α病毒（SAV），是一种单链正义RNA病毒，也是鲑鱼胰腺疾病和昏睡病的病原体。在本研究中，一株先前从球斑濑鱼中分离出的独特SAV菌株使用纳米孔测序技术进行了全基因组测序。为了与其他SAV菌株相比准确地研究该菌株的进化历史，进行了分区系统发育分析，以考虑单个基因和密码子位置进化速率的差异。与在整个基因组应用单一替换模型这种更常见的方法相比，对基因组比对进行分区几乎使系统发育树中观察到的分支长度增加了一倍，并显著提高了最佳拟合核苷酸替换模型的统计拟合度。基于基因组数据，可以有根据地认为本研究中检测的病毒菌株是一种新的SAV基因型。此外，本研究增加了越来越多发现SAV能感染非鲑科鱼类的研究数量，因此我们建议将该病毒物种名称修改为更具包容性的“鱼类α病毒”。
