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Diseases of Aquatic Organisms

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DAO 139:35-50 (2020)  -  DOI: https://doi.org/10.3354/dao03470

Pilchard orthomyxovirus (POMV). I. Characterisation of an emerging virus isolated from pilchards Sardinops sagax and Atlantic salmon Salmo salar

Peter G. Mohr1,*, Mark St. J. Crane1, John Hoad1, Lynette M. Williams1, David Cummins1, Matthew J. Neave1, Brian Shiell1, Gary Beddome1, Wojtek P. Michalski1, Grantley R. Peck1, Francisca Samsing2, James W. Wynne2, Sandra G. Crameri1, Alexander D. Hyatt1, Nicholas J. G. Moody1

1CSIRO Australian Animal Health Laboratory, 5 Portarlington Rd, East Geelong, Victoria 3220, Australia
2CSIRO Agriculture and Food, Aquaculture Program, Castray Esplanade, Battery Point, Tasmania 7004, Australia
*Corresponding author:

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.


KEY WORDS: Orthomyxovirus · Pilchard · Sardinops sagax · Atlantic salmon · Salmo salar · Australia


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Cite this article as: Mohr PG, Crane MStJ, Hoad J, Williams LM and others (2020) Pilchard orthomyxovirus (POMV). I. Characterisation of an emerging virus isolated from pilchards Sardinops sagax and Atlantic salmon Salmo salar. Dis Aquat Org 139:35-50. https://doi.org/10.3354/dao03470

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