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Diseases of Aquatic Organisms

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DAO 142:203-211 (2020)  -  DOI:

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

Andrew J. Tighe1,2,*, Michael D. Gallagher3, Jens Carlsson2, Iveta Matejusova4, Fiona Swords1, Daniel J. Macqueen3, Neil M. Ruane1

1Fish Health Unit, Marine Institute, Oranmore H91 R673, Ireland
2Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, University College Dublin, Dublin 4, Ireland
3The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
4Marine Scotland Science, Marine Laboratory, Aberdeen AB11 9DB, UK
*Corresponding author:

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’.

KEY WORDS: Nanopore · Phylogenetics · Whole genome sequencing · Viral nomenclature

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Cite this article as: Tighe AJ, Gallagher MD, Carlsson J, Matejusova I, Swords F, Macqueen DJ, Ruane NM (2020) Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7). Dis Aquat Org 142:203-211.

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