Abstract
Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (Salmo salar). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q266→L266 substitution or insertion next to the putative cleavage site (R267) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA outbreak at the same farming site three weeks later, and compared the mutant spectra. As the UDPS data shows the presence of both HE genotypes at both sampling times, and the outbreak strain was unlikely to be directly related to the HPR0 strain, this is the first report of a double infection with HPR0s and vISAVs. For F amplicon reads, mutation frequencies generating L266 codons in screening samples and Q266 codons in outbreak samples were not higher than at any random site. We suggest quasispecies heterogeneity as well as RNA structural properties are linked to transition to virulence. More specifically, a mechanism where selected single point mutations in the full-length HPR alter the RNA structure facilitating single- or sequential deletions in this region is proposed. The data provides stronger support for the deletion hypothesis, as opposed to recombination, as the responsible mechanism for generating the sequence deletions in HE.
Highlights
Infectious salmon anaemia virus (ISAV) is an orthomyxovirus that has caused systemic infection and disease in farmed Atlantic salmon (Salmo salar) in Norway, Canada, Scotland, Shetland Islands, the Faroe Islands, USA and Chile [1,2,3,4,5,6,7,8]
This paper describes the results obtained from ultra-deep pyrosequencing (UDPS) of the variable regions in ISAV HE- and F genes from non-virulent HPR0-positive fish collected from screening, and a virulent strain sampled from an ISA outbreak at the same farming site three weeks later
UDPS of non-virulent ISAV HPR0- and virulent ISAV strains is presented for the first time
Summary
Infectious salmon anaemia virus (ISAV) is an orthomyxovirus that has caused systemic infection and disease in farmed Atlantic salmon (Salmo salar) in Norway, Canada, Scotland, Shetland Islands, the Faroe Islands, USA and Chile [1,2,3,4,5,6,7,8]. The. HEs from different virulent ISAV strains (vISAVs) often vary in length as determined by the size of their highly polymorphic region (HPR) located in the stalk immediately upstream of the transmembrane domain of the protein. The deletions in the HE stalk region could be analogues to the varying lengths in the influenza A virus neuraminidase stalk, which has been associated with host switching [15,16,17,18]. A shortening of the HE stalk could affect the functional balance between the HE receptor-binding and -destroying activities similar to that found between the hemagglutinin and neuraminidase of influenza A viruses through a number of studies [19,20,21,22,23]
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