Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Abstract

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages

“…Consistent with a recent study [34], all Norwegian SAV2 sequences were monophyletic and descended from Scottish SAV2 sequences (Figures 4A and S2). According to the Bayesian tree (Figure 4A), which employed a relaxed uncorrelated molecular clock model [49] assuming constant viral population size, the most recent common ancestor (MRCA) of Norwegian SAV2 existed during 2010 (95% HPD: 2009-2011).…”

“…To demonstrate the sensitivity of our approach, we mapped the data to two different SAV2 genomes, one from an Atlantic salmon sampled in 2007 (accession: MH708652) [37] and the other from a rainbow trout sampled in 1997 (accession: AJ316246). While these sequences share 97.9% nucleotide identity, almost all mapping was to MH708652 (Figure 3A), which is expected as Norwegian SAV2 genomes are more closely related to this sequence than AJ316246 [34]. Mean mapping depth to SAV2 was 1010.8× across the 94 samples (range: 12.5× to 4392.3×), while mean mapping coverage was 96.3% (range: 74.5% to 99.5%), with 86 samples showing >90% coverage (Table S4).…”

“…PD has been present in Norway since the 1980s and is thought to have been exclusively caused by SAV3 until SAV2 was detected during an outbreak in 2010 [32,33]. SAV2 was likely initially transmitted to mid-Norway from Scotland, where SAV2 is a common PD-causing subtype [34]. This may have occurred via industry well boat activity, though transmission from wild reservoir species cannot yet be ruled out [34].…”

“…SAV2 was likely initially transmitted to mid-Norway from Scotland, where SAV2 is a common PD-causing subtype [34]. This may have occurred via industry well boat activity, though transmission from wild reservoir species cannot yet be ruled out [34]. SAV2 and SAV3 are defined as separate endemics in Norway, tolerated in largely non-overlapping regions within a wider endemic PD zone, stretching from the southern end of Norway to Flatanger in Trøndelag [35] (Figure 1).…”

Introduction and temporospatial tracing of piscine orthoreovirus‐1 (PRV‐1) in Norwegian farmed Atlantic salmon (Salmo salar) after local fallowing

“…The same genogroup of the virus was found at different sites in the area, suggesting the potential spread of infection through water. Well boats have also been identified as a potential route of transmission for disease in aquaculture (Hjortaas et al, 2021;Lyngstad et al, 2015). However, investigation into the introduction and dissemination routes of PRV-1 in a field setting has been limited (Pettersen et al, 2015).…”