Prevalence and genotypes of infectious salmon anaemia virus (ISAV) in returning wild Atlantic salmon (<i>Salmo salar</i> L.) in northern Norway

Madhun, Abdullah Sami; Mæhle, Stig; Wennevik, Vidar; Karlsbakk, Egil

doi:10.1111/jfd.13021

Cited by 14 publications

(13 citation statements)

References 22 publications

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“…Viruses of this family share similar strategies of infection, using haemagglutinin activity to enter the cells and fusion activity to escape the lysosome, followed by viral RNA replication in the nucleus of the host cell and modulation of host immune responses [ 7 – 9 ]. The genome of ISAV is divided in 8 segments that encode at least 10 different proteins, and the virus can be divided in two groups, the low virulence ISAV-HPR0 and the virulent ISAV-HPRΔ, which has a deletion in the highly polymorphic region of the haemagglutinin-esterase gene [ 10 ]. ISA is classified as a list II disease by the EU fish health directive and as a notifiable disease by the World Organisation for Animal Health [ 11 ], which means that entire stocks have to be culled upon detection of the virus to avoid the spread to nearby farms.…”

Section: Introductionmentioning

confidence: 99%

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

et al. 2021

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Background Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. Results A total of 2833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1353 animals were genotyped using a 55 K SNP array, and the estimate of heritability for the trait of binary survival was 0.13–0.33 (pedigree-genomic). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome Ssa13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated in infected fish, while several metabolic pathways were up-regulated. The interferon pathway showed little evidence of up-regulation at 7 days post infection but was mildly activated at 14 days, suggesting a potential crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish. Conclusions ISAV resistance shows moderate heritability with a polygenic architecture, but a significant QTL was detected on chromosome 13. A mild up-regulation of the interferon pathway characterises the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.

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Section: Introductionmentioning

confidence: 99%

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

et al. 2021

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“…Viruses of this family share similar strategies of infection, using haemagglutinin activity to enter the cells and fusion activity to escape the lysosome, followed by viral RNA replication in the nucleus of the host cell and modulation of host immune responses [16][17][18]. The genome of ISAV is divided in 8 segments that encode at least 10 different proteins, and the virus can be divided in two groups, the low virulence ISAV-HPR0 and the virulent ISAV-HPRΔ, which has a deletion in the highly polymorphic region of the haemagglutininesterase gene [19]. Currently there are no effective treatments against ISAV, and available vaccines are typically only partially protective [20].…”

Section: Introductionmentioning

confidence: 99%

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

Gervais

Barría

Papadopoulou

et al. 2020

Preprint

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Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon breeders and producers worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV in commercial strains of Atlantic salmon is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. A total of 2,833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1,353 animals were genotyped using a 55K SNP array, and the estimate of heritability for the trait of binary survival was 0.33 (±0.04). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome 13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4,927 and 2,437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated, while several metabolic pathways were up-regulated in infected fish compared to controls. The interferon pathway was mildly activated at 7 days and showed no sign of up-regulation at 14 days post infection, implying a crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance (4 high resistance and 4 low resistance animals per time point) highlighted TRIM25 as being up-regulated in resistant fish, suggesting it may be a key antiviral gene involved in the functional genetic basis of resistance to ISAV.

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“…Subsequently, HPR0 G4 was detected in Scotland [44] and in the Faroe Island [4]. The G4 variant has not been detected in Norwegian aquaculture, but was recently reported from wild caught Atlantic salmon [17,24].…”

Section: Viral Fitness Of Hpr0 In G2 Vs G4mentioning

confidence: 98%

“…HPR0 has been detected in wild anadromous Atlantic salmon in Norway [16,17,24], Scotland [9] and Chile [25]. Because new HPR∆ variants may arise from HPR0 [14,26], its common occurrence and widespread distribution in farmed [4,14,16,17,26] and wild [17,24] Atlantic salmon makes it a potential risk factor for the emergence of new HPR∆ and ISA disease. Hence, understanding HPR0's transmission mode and route is fundamental for proper management and mitigation strategies in Atlantic salmon farming.…”

Section: Introductionmentioning

confidence: 99%

No Evidence of the Vertical Transmission of Non-Virulent Infectious Salmon Anaemia Virus (ISAV-HPR0) in Farmed Atlantic Salmon

Christiansen

Petersen

Dahl

et al. 2021

Viruses

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The nonvirulent infectious salmon anaemia virus (ISAV-HPR0) is the putative progenitor for virulent-ISAV, and a potential risk factor for the development of infectious salmon anaemia (ISA). Understanding the transmission dynamics of ISAV-HPR0 is fundamental to proper management and mitigation strategies. Here, we demonstrate that ISAV-HPR0 causes prevalent and transient infections in all three production stages of Atlantic salmon in the Faroe Islands. Phylogenetic analysis of the haemagglutinin-esterase gene from 247 salmon showed a clear geographical structuring into two significantly distinct HPR0-subgroups, which were designated G2 and G4. Whereas G2 and G4 co-circulated in marine farms, Faroese broodfish were predominantly infected by G2, and smolt were predominantly infected by G4. This infection pattern was confirmed by our G2- and G4-specific RT-qPCR assays. Moreover, the HPR0 variants detected in Icelandic and Norwegian broodfish were never detected in the Faroe Islands, despite the extensive import of ova from both countries. Accordingly, the vertical transmission of HPR0 from broodfish to progeny is uncommon. Phylogenetic and statistical analysis suggest that HPR0 persists in the smolt farms as “house-strains”, and that new HPR0 variants are occasionally introduced from the marine environment, probably by HPR0-contaminated sea-spray. Thus, high biosecurity—including water and air intake—is required to avoid the introduction of pathogens to the smolt farms.

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Prevalence and genotypes of infectious salmon anaemia virus (ISAV) in returning wild Atlantic salmon (Salmo salar L.) in northern Norway

Cited by 14 publications

References 22 publications

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

No Evidence of the Vertical Transmission of Non-Virulent Infectious Salmon Anaemia Virus (ISAV-HPR0) in Farmed Atlantic Salmon

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