In vivo virulence and genomic comparison of infectious Salmon Anaemia Virus isolates from Atlantic Canada

Abstract

The infectious salmon anaemia virus (ISAV) is capable of causing a significant disease in Atlantic salmon, which has resulted in considerable financial losses for salmon farmers around the world. Since the first detection of ISAV in Canada in 1996, it has been a high priority for aquatic animal health management and surveillance programmes have led to the identification of many genetically distinct ISAV isolates of variable virulence. In this study, we evaluated the virulence of three ISAV isolates detected in Atlantic Canada in 2012 by doing in vivo-controlled disease challenges with two sources of Atlantic salmon. We measured viral loads in fish tissues during the course of infection. Sequences of the full viral RNA genomes of these three ISAV isolates were obtained and compared to a high-virulence and previously characterized isolate detected in the Bay of Fundy in 2004, as well as a newly identified ISAV NA-HPR0 isolate. All three ISAV isolates studied were shown to be of low to mid-virulence with fish from source A having a lower mortality rate than fish from source B. Viral load estimation using an RT-qPCR assay targeting viral segment 8 showed a high degree of similarity between tissues. Through genomic comparison, we identified various amino acid substitutions unique to some isolates, including a stop codon in the segment 8 ORF2 not previously reported in ISAV, present in the isolate with the lowest observed virulence.

First report of successful isolation of a HPR0‐like variant of the infectious salmon anaemia virus (ISAV) using cell culture

“…On S5, a prerequisite of virulence seems to be a Q 266 →L 266 substitution or Q 266 with an insertion close to the putative cleavage site (Devold, 2006 ; Markussen et al., 2008 ). Association of these markers to virulent variants of ISAV has been supported over the years (Cárdenas et al., 2019 ; LeBlanc et al., 2018 ). This is the first report of the successful isolation in cell culture, supported with data, of a natural HPR0 variant, as defined by current genotyping, but is also the first report of a natural ISAV variant possessing a S6 typical of non‐virulent variants (no deletion in the HPR) and a S5 typical of virulent variants (Q 266 with an insertion).…”

Investigation of laboratory methods for characterization of aquatic viruses in fish infected experimentally with infectious salmon anemia virus

“…Table 1). 30 Reference segment coverage of assembled contigs ranged from 65.0–102% because some of the assembled contigs were longer than the reference accession lengths and some shorter as a result of markedly lower coverage on both platforms across the shortest ISAV segment. To elucidate whole-genome comparison between our draft genome and publicly available whole ISAV genomes, we mapped the data to GenBank KX424582–KX424589 and found that raw reads aligned to these 8 segments with high concordance, yielding a consensus genome with ≥ 14 high-quality SNVs—5 of which confer amino acid substitutions—with GridION sequencing depth > 100× and/or MiSeq depth > 50× (Suppl.…”

Accelerated ISAV replication detection by cell culture methods combined with time‐monitoring RT‐qPCR

“…Segment six houses a highly polymorphic region (HPR) which is commonly used for genotyping (Aamelfot, Dale, & Falk, ; Cunningham, Gregory, Black, Simpson, & Raynard, ; Fourrier et al., ; Mjaaland et al., ; Ritchie et al., ). It is accepted that the HPR genotype is at least partially responsible for ISAV strain virulence, although other virulence‐related factors have also been suggested (Kibenge et al., ; LeBlanc, Leadbeater, Laflamme, & Gagne, ; Markussen et al., ).…”

“…virulence, although other virulence-related factors have also been suggested (Kibenge et al, 2007;LeBlanc, Leadbeater, Laflamme, & Gagne, 2018;Markussen et al, 2008).…”