Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture

Gallagher, Michael D.; Karlsen, Marius; Petterson, Elin; Haugland, Øyvind; Matějusová, Iveta; Macqueen, Daniel J.

doi:10.3389/fmicb.2020.00740

Cited by 5 publications

(11 citation statements)

References 41 publications

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“…In 2014, analysis of a large number of SAV3 genomes showed that this particular genotype was introduced to Norwegian aquaculture as a single event from an unknown source of infection [ 23 ]. A more recent analysis of the genetic diversity of SAV3 in selected areas of Norway demonstrated repeated seeding events in Vestland County [ 24 ], through a process that hypothetically may have contributed to the country-wide spread of SAV3 since the first introduction.…”

Section: Introductionmentioning

confidence: 99%

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

Hjortaas

Fringuelli

Monjane

et al. 2021

Viruses

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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.

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Section: Introductionmentioning

confidence: 99%

“…Although increasing in number [ 11 , 24 , 25 , 26 ], full-length or near full-length SAV sequence data represent only a minor proportion of the total publicly available sequence data for SAV. Among the approximately seventy publicly available full-length SAV genomes, only twelve represent SAV2, thirty-five SAV3 and fourteen SAV1.…”

Section: Introductionmentioning

confidence: 99%

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

Hjortaas

Fringuelli

Monjane

et al. 2021

Viruses

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“…While it is recognized that genomic epidemiology can deliver much to support disease control efforts in aquaculture [11] and other sectors [12], large-scale genomic sequencing to monitor aquaculture pathogens is not a widespread practice, even for high-value species. Nonetheless, several studies highlight the value of genomic epidemiology for linking viral genetic diversity to disease outbreaks and identifying viral transmission scenarios [13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

“…We used nanopore sequencing to generate SAV2 genomic sequences from infected fish sampled between 2018 and 2020 from 27 sampling sites spanning 10 major production areas (Figure 1). Our previous work has shown that nanopore sequencing of SAV and other fish viruses offers a rapid and cost-effective approach with extremely high consensus accuracy, which can be used to identify complex infections involving different viral strains [14,37].…”

Section: Introductionmentioning

confidence: 99%

“…Viruses 2021, 13, x FOR PEER REVIEW 3 of 17 other fish viruses offers a rapid and cost-effective approach with extremely high consensus accuracy, which can be used to identify complex infections involving different viral strains [14,37]. Using extensive new nanopore data alongside existing SAV genome sequence data, we reconstruct the phylogenetic diversity of SAV2 circulating in recent Norwegian aquaculture, revealing plausible geographical origins for recent SAV2 outbreaks outside the SAV2 endemic zone, and identify novel ancestral lineages of SAV3 in fish coinfected with both SAV2 and SAV3.…”

Section: Introductionmentioning

confidence: 99%

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

Macqueen

Eve

Gundappa

et al. 2021

Viruses

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Viral disease poses a major barrier to sustainable aquaculture, with outbreaks causing large economic losses and growing concerns for fish welfare. Genomic epidemiology can support disease control by providing rapid inferences on viral evolution and disease transmission. In this study, genomic epidemiology was used to investigate salmonid alphavirus (SAV), the causative agent of pancreas disease (PD) in Atlantic salmon. Our aim was to reconstruct SAV subtype-2 (SAV2) diversity and transmission dynamics in recent Norwegian aquaculture, including the origin of SAV2 in regions where this subtype is not tolerated under current legislation. Using nanopore sequencing, we captured ~90% of the SAV2 genome for n = 68 field isolates from 10 aquaculture production regions sampled between 2018 and 2020. Using time-calibrated phylogenetics, we infer that, following its introduction to Norway around 2010, SAV2 split into two clades (SAV2a and 2b) around 2013. While co-present at the same sites near the boundary of Møre og Romsdal and Trøndelag, SAV2a and 2b were generally detected in non-overlapping locations at more Southern and Northern latitudes, respectively. We provide evidence for recent SAV2 transmission over large distances, revealing a strong connection between Møre og Romsdal and SAV2 detected in 2019/20 in Rogaland. We also demonstrate separate introductions of SAV2a and 2b outside the SAV2 zone in Sognefjorden (Vestland), connected to samples from Møre og Romsdal and Trøndelag, respectively, and a likely 100 km Northward transmission of SAV2b within Trøndelag. Finally, we recovered genomes of SAV2a and SAV3 co-infecting single fish in Rogaland, involving novel SAV3 lineages that diverged from previously characterized strains >25 years ago. Overall, this study demonstrates useful applications of genomic epidemiology for tracking viral disease spread in aquaculture.

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Antiviral Innate Immune Responses: Infectious Pancreatic Necrosis Virus and Salmonid Alphavirus

Gamil

Gadan

et al. 2022

Principles of Fish Immunology

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Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture

Cited by 5 publications

References 41 publications

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

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

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

Antiviral Innate Immune Responses: Infectious Pancreatic Necrosis Virus and Salmonid Alphavirus

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