ABSTRACT: An orthomyxo-like virus was first isolated in 1998 as an incidental discovery from pilchards Sardinops sagax collected from waters off the South Australian coast. In the following 2 decades, orthomyxo-like viruses have been isolated from healthy pilchards in South Australia and Tasmania. In 2006, an orthomyxo-like virus was also isolated from farmed Atlantic salmon Salmo salar in Tasmania during routine surveillance and, again, from 2012 onwards from diseased Atlantic salmon. Using transmission electron microscopy, these viruses were identified as belonging to the family Orthomyxoviridae. To further characterise the viruses, the genomes of 11 viral isolates were sequenced. The open reading frames (ORFs) that encode 10 putative proteins from 8 viral genome segments were assembled from Illumina MiSeq next generation sequencing (NGS) data. The complete genome of a 2014 isolate was also assembled from NGS, RNA-sequencing (RNA-seq) data, that included conserved motifs that shared commonalities with infectious salmon anaemia virus, rainbow trout orthomyxovirus and Influenzavirus A. The presence of 8 viral proteins translated from genome segments was confirmed by mass spectrometric analysis including 2 novel proteins with no known orthologs. Sequence analysis of the ORFs, non-coding regions and proteins indicated that the viruses had minimal diversity and hence were named pilchard orthomyxovirus (POMV), based on the fish host species of its first isolation. The low homology of POMV proteins with previously characterised orthomyxoviruses suggests that POMV is the first virus to be characterised from a new genus within the Orthomyxoviridae. To facilitate more rapid detection and subsequent diagnostic confirmation of POMV infections, TaqMan and conventional nested PCRs were designed.

中文翻译：

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Pilchard正粘病毒（POMV）。I.从沙丁鱼Sardinops sagax和大西洋鲑Salmo salar中分离出的一种新兴病毒的特征。

摘要：orthomyxo像病毒于1998年首次分离自沙丁鱼偶然发现Sardinops sagax从关南澳大利亚海岸水域收集。在随后的20年中，从南澳大利亚州和塔斯马尼亚州的健康沙丁鱼中分离出了类正粘病毒。2006年，在例行监视期间，还从塔斯马尼亚州养殖的大西洋鲑鱼Salmo鲑鱼中分离出一种正粘病毒，从2012年起，再次从患病的大西洋鲑鱼中分离出了这种病毒。使用透射电子显微镜，这些病毒被鉴定为属于正粘病毒科。为了进一步表征病毒，对11种病毒分离株的基因组进行了测序。从Illumina MiSeq下一代测序（NGS）数据中组装了编码来自8个病毒基因组片段的10个推定蛋白质的开放阅读框（ORF）。还从NGS，RNA测序（RNA-seq）数据中收集了2014年分离株的完整基因组，其中包括与传染性鲑鱼贫血病毒，虹鳟正粘病毒和甲型流感病毒具有共同点的保守基序。。通过质谱分析确认了从基因组片段翻译的8种病毒蛋白的存在，包括2种未知直向同源物的新型蛋白。ORF，非编码区和蛋白质的序列分析表明，该病毒具有最小的多样性，因此基于首次分离的鱼类宿主物种，被命名为沙丁鱼正粘病毒（POMV）。POMV蛋白与以前的正粘病毒的低同源性表明，POMV是第一个从正粘病毒科的新属中鉴定的病毒。为了促进POMV感染的更快速检测和随后的诊断确认，设计了TaqMan和常规的巢式PCR。