DAO 66:105-111 (2005)  -  doi:10.3354/dao066105

Nucleotide sequence variation in salmonid alphaviruses from outbreaks of salmon pancreas disease and sleeping disease

J. H. Weston1, D. A. Graham2, E. Branson3, H. M. Rowley2, I. W. Walker2, V. A. Jewhurst1, H. L. Jewhurst1, D. Todd2,*

1The Queen’s University of Belfast, Department of Veterinary Sciences, Stormont, Belfast BT4 3SD, UK
2Department of Agriculture and Rural Development, Veterinary Sciences Division, Stormont, Belfast BT4 3SD, UK
3Red House Farm, Llanvihangel, Monmouth NP25 5HL, UK
*Corresponding author. Email:

ABSTRACT: We compared 18 salmonid alphaviruses (SAV) including the reference F93-125 salmon pancreas disease virus (SPDV) and S49p sleeping disease virus (SDV) isolates by nucleotide sequence analyses of regions within the E1, nsP4 and nsP3 genes, and found these to comprise 3 distinct groups, which we have designated Subtypes 1, 2 and 3: Subtype 1, which comprised SAVs with sequences closely similar to the reference SPDV isolate, included SAVs from pancreas disease (PD) outbreaks in farmed salmon in Ireland and Scotland over a 10 yr period; viruses from recent outbreaks of sleeping disease (SD) in freshwater-reared trout farmed in England, Scotland and France were closely similar to and were grouped with the reference SDV isolate in Subtype 2; 3 viruses isolated from PD-affected salmon in Norway were genetically different from viruses belonging to Subtypes 1 and 2 and have been assigned to Subtype 3; 1 virus isolated from PD-affected salmon in the Western Isles, Scotland, in 2003 showed consistent nucleotide sequence differences from SAV Subtypes 1, 2 and 3, but was more closely related to the Subtype 1 SAVs. The occurrence of the different subtype SAVs appeared to have a geographical basis, which may prove useful in future molecular epidemiology studies of SAV-induced disease outbreaks.

KEY WORDS: Salmon pancreas disease · Sleeping disease · Salmonid alphavirus · SAV · Subtypes 1, 2 and 3

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