Alphavirus infections in salmonids--a review

Virus-specific antibody secreting cells reside in the peritoneal cavity and systemic immune sites of Atlantic salmon (Salmo salar) challenged intraperitoneally with salmonid alphavirus

The development and persistence of antibody secreting cells (ASC) after antigenic challenge remain inadequately understood in teleosts. In this study, intraperitoneal (ip) injection of Atlantic salmon (Salmo salar) with salmonid alphavirus (WtSAV3) increased the total ASC response, peaking 3-6 weeks post injection (wpi) locally in the peritoneal cavity (PerC) and in systemic lymphoid tissues, while at 13 wpi the response was only elevated in PerC. At the same time point a specific ASC response was induced by WtSAV3 in PerC and systemic tissues, with the highest frequency in PerC, suggesting a local role. Inactivated SAV (InSAV1) induced comparatively lower ASC responses in all sites, and specific serum antibodies were only induced by WtSAV3 and not by InSAV1. An InSAV1 boost did not increase these responses. Expression of immune marker genes implies a role for PerC adipose tissue in the PerC immune response. Overall, the study suggests the Atlantic salmon PerC as a secondary immune site and an ASC survival niche.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU)2016/429): Infection with salmonid alphavirus (SAV)

Infection with salmonid alphavirus (SAV) was assessed according to the criteria of the Animal Health Law (AHL), in particular the criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as laid out in Article 9 and Article 8 for listing animal species related to infection with SAV. The assessment was performed following the ad hoc method on data collection and assessment developed by AHAW Panel and already published. The outcome reported is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with an uncertain outcome. According to the assessment, it was uncertain whether infection with salmonid alphavirus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (50-80% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that infection with salmonid alphavirus does not meet the criteria in Section 1 (Category A; 5-10% probability of meeting the criteria) and it is uncertain whether it meets the criteria in Sections 2, 3, 4 and 5 (Categories B, C, D and E; 50-90%, probability of meeting the criteria). The animal species to be listed for infection with SAV according to Article 8 criteria are provided.

Characterization of early phases of cardiomyopathy syndrome pathogenesis in Atlantic salmon (Salmo salar L.) through various diagnostic methods

Since the first description of cardiomyopathy syndrome (CMS) in Atlantic salmon, in 1985, the disease caused by piscine myocarditisvirus (PMCV) has become a common problem in Atlantic salmon farming, not only in Norway, but also in other salmon farming countries like Scotland and Ireland. In the last years, CMS has been ranked as the most important salmon viral disease in Norway regarding both mortality and economic losses. Detailed knowledge of infection and pathogenesis is still lacking, a decade after the causal agent was first described, and there is a need for a wider range of methods/tools for diagnostic and research purposes. In this study, we compared the detection of PMCV- and CMS-related tissue lesions using previously used and well-known methods like histopathology and real-time RT-PCR to immunohistochemistry (IHC), a less used method, and a new method, RNAscope in situ hybridization. Tissue samples of three different cardiac compartments, mid-kidney and skin/muscle tissue were compared with non-lethal parallel samplings of blood and mucus. The development of pathological cardiac lesions observed in this experiment was in accordance with previous descriptions of CMS. Our results indicate a viremic phase 10- to 20-day post-challenge (dpc) preceding the cardiac lesions. In this early phase, virus could also be detected in relatively high amount in mid-kidney by real-time RT-PCR. Plasma and/or mid-kidney samples may, therefore, be candidates to screen for early-phase PMCV infection. The RNAscope in situ hybridization method showed higher sensitivity and robustness compared with the immunohistochemistry and may be a valuable support to histopathology in CMS diagnostics, especially in cases of untypical lesions or mixed infections.

LC-qTOF-MS analysis of fish immune organs reveals the distribution of amino acids in response to metabolic adaptation of the survival phenotype in grouper against Vibrio infection

Epinephelus fuscoguttatus is economically crucial to various Southeast Asia countries where they are reared in fish farms to meet the demand for supply. However, a systemic infectious disease known as vibriosis has steadily and extensively affected the fish farming industry. The disease is caused by Vibrio spp., which are pathogenic gram-negative bacteria. This study focused on understanding the host's metabolic adaptation against Vibrio vulnificus infection, which features a survival phenotype, by profiling the metabolites in grouper fingerlings that survived the experimental infection. Mapping of the pathways is crucial to explain the roles of metabolites in fish immunity. A solvent extraction method was used on the grouper's immune organs (gills, liver and spleen) prior to Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry (LC-qTOF-MS) analysis. The metabolites identified in fingerlings that survived experimental infections were mostly amino acids (primary metabolites). Glutamine (0.44%), alanine (0.68%), phenylalanine (2.63%) and tyrosine (2.60%) were highly abundant in survived-infected gills. Aspartic acid (13.57%) and leucine (4.01%) were highly abundant in the livers of the survived-infected fish and lysine was highly abundant in both gills (2.94%) and liver (3.64%) of the survived-infected fish. Subsequent bioinformatics analysis revealed the involvement of the identified functional amino acids in various immune-related pathways. The current findings facilitate the comprehension of the metabolic adaptation of grouper fingerlings that exhibited a survival phenotype against Vibrio infection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03269-1.

Development and Evaluation of DNA Vaccine Against Salmonid Alphavirus

Despite vaccination, pancreas disease (PD) caused by salmonid alphavirus (SAV) has been the economically most important virus disease in salmon farming in Ireland, Scotland, and Norway. A vaccine based on DNA plasmid has been authorized to be used in Norwegian aquaculture since 2018. DNA vaccination of plasmids expressed subcellular viral proteins have been shown its particular protective effect against SAV3 that surface expression of the E2 protein with the whole viral protein construct, yielding a more effective vaccine. The chapter describes methods to design and test the sublocalization of expressed viral protein and the performance evaluation of vaccines against SAV3 infection in Atlantic salmon.

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

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.

Effect of vaccines against pancreas disease in farmed Atlantic salmon

Pancreas disease (PD) caused by salmonid alphavirus (SAV) continues to negatively impact salmon farming. To assess the effect on growth and mortality of three vaccines against PD, two controlled field designs were employed: one controlled field study with individual marked fish (PIT tag) assessing three PD vaccines and three controls groups, and a second controlled field study with group marked fish (Maxilla) comparing two PD vaccines against controls. In addition, a descriptive study using whole cages compared fish immunized with two different PD vaccines against controls. The target populations experienced a natural PD outbreak where both SAV 2 and SAV 3 were identified. Only one of the PD vaccines provided statistically significant improvements in harvest weight of 0.43 kg (CI: 0.29-0.57) and 0.51 kg (CI: 0.36-0.65) compared with the control in the PIT tag and the Maxilla study, respectively. In the latter, a significant reduction in mortality of 1.31 (CI:0.8-1.8) per cent points was registered for the same vaccine compared with controls. These results aligned with the growth and PD-specific mortality registered in the descriptive Cage study. The data in this study show a difference in the efficacy of PD vaccines in farmed Atlantic salmon.

Ultrastructural insights into the replication cycle of salmon pancreas disease virus (SPDV) using salmon cardiac primary cultures (SCPCs)

Salmon pancreas disease virus (SPDV) has been affecting the salmon farming industry for over 30 years, but despite the substantial amount of studies, there are still a number of recognized knowledge gaps, for example in the transmission of the virus. In this work, an ultrastructural morphological approach was used to describe observations after infection by SPDV of an ex vivo cardiac model generated from Atlantic salmon embryos. The observations in this study and those available on previous ultrastructural work on SPDV are compared and contrasted with the current knowledge on terrestrial mammalian and insect alphaviral replication cycles, which is deeper than that of SPDV both morphologically and mechanistically. Despite their limitations, morphological descriptions remain an excellent way to generate novel hypotheses, and this has been the aim of this work. This study has used a target host, ex vivo model and resulted in some previously undescribed features, including filopodial membrane projections, cytoplasmic stress granules or putative intracytoplasmic budding. The latter suggests a new hypothesis that warrants further mechanistic research: SPDV in salmon may have retained the capacity for non-cytolytic (persistent) infections by intracellular budding, similar to that noted in arthropod vectors of other alphaviruses. In the notable absence of a known intermediate host for SPDV, the presence of this pattern suggests that both cytopathic and persistent infections may coexist in the same host. It is our hope that the ultrastructural comparison presented here stimulates new research that brings the knowledge on SPDV replication cycle up to a similar level to that of terrestrial alphaviruses.

Characterization of an outbreak of cardiomyopathy syndrome (CMS) in young Atlantic salmon, Salmo salar L

Cardiomyopathy syndrome (CMS) is the most common viral cardiac disease in Norwegian Atlantic salmon farming and typically affects large, market size fish. Only six months after seawater transfer, Atlantic salmon were diagnosed with CMS at a fish farm in the south-western part of Norway. Due to the unexpected young age and the remarkable large amounts of virus-specific RNA (Ct <10), the fish group was monitored with five additional samplings until slaughtered almost 10 months later. At three weeks after the first CMS diagnosis (weeks post-diagnosis, wpd) and at slaughter (39 wpd), more comprehensive samplings were performed of the study cage, with specific focus on three different cardiac compartments. The clinical, autopsy and histopathological findings at first diagnosis and at all succeeding samplings were similar to previous descriptions of typical CMS. A slightly elevated mortality was observed in the cage with diseased fish at the time of the first CMS diagnosis and continued throughout the study. The prevalence and load of PMCV-specific RNA in the fish remained high until slaughtering, with similar amounts in all sampled cardiac compartments. No fish from the other five cages at the site were diagnosed with CMS, until fish sampled from the last cage at the site were diagnosed 10 weeks after slaughtering of the study cage (49 wpd). Sequence analysis of the PMCV on the site showed that the outbreak virus was similar to PMCV variants previously sequenced from Norwegian field outbreaks. In conclusion, CMS in young Atlantic salmon had clinical signs and histopathological cardiac lesions typical for the disease, and diseased fish could be found in the study cage until slaughtering.

Effect of two constant light regimens on antibody profiles and immune gene expression in Atlantic salmon following vaccination and experimental challenge with salmonid alphavirus

Before seawater transfer, farmed Atlantic salmon are subjected to treatments that may affect the immune system and susceptibility to pathogens. E.g., exposure to constant light (CL) stimulates smoltification, which prepares salmon to life in sea water, but endocrine changes in this period are associated with suppression of immune genes. Salmon are vaccinated towards end of the freshwater period to safeguard that adequate vaccine efficacy is achieved by the time the fish is transferred to sea. In the present study, we investigated how the responses to vaccination and viral infection varied depending on the time of CL onset relative to vaccination. The salmon were either exposed to CL two weeks prior to vaccination (2-PRI) or exposed to CL at the time of vaccination (0-PRI). A cohabitant challenge with salmonid alphavirus, the causative agent of pancreatic disease, was performed 9 weeks post vaccination. The immunological effects of the different light manipulation were examined at 0- and 6-weeks post vaccination, and 6 weeks post challenge. Antibody levels in serum were measured using a serological bead-based multiplex panel as well as ELISA, and 92 immune genes in heart and spleen were measured using an integrated fluidic circuit-based qPCR array for multiple gene expression. The 2-PRI group showed a moderate transcript down-regulation of genes in the heart at the time of vaccination, which were restored 6 weeks after vaccination (WPV). Conversely, at 6WPV a down-regulation was seen for the 0-PRI fish. Moreover, the 2-PRI group had significantly higher levels of antibodies binding to three of the vaccine components at 6WPV, compared to 0-PRI. In response to SAV challenge, transcription of immune genes between 2-PRI and 0-PRI was markedly dissimilar in the heart and spleen of control fish, but no difference was found between vaccinated salmon from the two CL regimens. Thus, by using labor-saving high throughput detection methods, we demonstrated that light regimens affected antibody production and transcription of immune genes in non-vaccinated and virus challenged salmon, but the differences between the light treatment groups appeared eliminated by vaccination.

Omics Strategies in Current Advancements of Infectious Fish Disease Management

Aquaculture is an important industry globally as it remains one of the significant alternatives of animal protein source supplies for humankind. Yet, the progression of this industry is being dampened by the increasing rate of fish mortality, mainly the outbreak of infectious diseases. Consequently, the regress in aquaculture ultimately results in the economy of multiple countries being affected due to the decline of product yields and marketability. By 2025, aquaculture is expected to contribute approximately 57% of fish consumption worldwide. Without a strategic approach to curb infectious diseases, the increasing demands of the aquaculture industry may not be sustainable and hence contributing to the over-fishing of wild fish. Recently, a new holistic approach that utilizes multi-omics platforms including transcriptomics, proteomics, and metabolomics is unraveling the intricate molecular mechanisms of host-pathogen interaction. This approach aims to provide a better understanding of how to improve the resistance of host species. However, no comprehensive review has been published on multi-omics strategies in deciphering fish disease etiology and molecular regulation. Most publications have only covered particular omics and no constructive reviews on various omics findings across fish species, particularly on their immune systems, have been described elsewhere. Our previous publication reviewed the integration of omics application for understanding the mechanism of fish immune response due to microbial infection. Hence, this review provides a thorough compilation of current advancements in omics strategies for fish disease management in the aquaculture industry. The discovery of biomarkers in various fish diseases and their potential advancement to complement the recent progress in combatting fish disease is also discussed in this review.

Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes

Pancreas Disease (PD) is a viral disease caused by Salmonid Alphavirus (SAV). It affects farmed salmonids in the North Atlantic, and leads to reduced feed intake and increased mortality with reduced production and welfare as a consequence. In 2013, the estimated cost of an outbreak on an average salmon farm was about 6.6 mil €. In Norway, PD has been notifiable since 2008, and regulations to mitigate disease spread are in place. However, despite the regulations, 140-170 farms are affected by PD every year. The aquaculture industry is growing continuously, introducing farms in new geographical areas, and fish are moved between hydrographically separated zones for trade and slaughter. All such movements and relocations need to be approved by the competent authorities. Thus, there is a demand for support to farmers and competent authorities when making decisions on disease management and especially on the effect of moving infected fish. We have used a disease-transmission model for outbreak-simulation in real time for assessing the probability of disease transmission from a farm that gets infected with PD. We have also simulated the effects of three different control-regimes: no stamping-out, delayed stamping-out or immediate stamping-out, on the transmission of PD to surrounding farms. Simulations showed that the immediate stamping out of an infected farm led to effective containment of an outbreak. No stamping out led to up to 32.1% of farms within 100 km of the index farm to become effected. We have used real production data for the model building and the scenario simulations, and the results illustrate that a risk assessment of horizontal disease transmission must be undertaken on a case-by-case basis, because the time and place of the outbreak has a large influence on the risk of transmission.

Establishment and Characterization of a Novel Gill Cell Line, LG-1, from Atlantic Lumpfish (Cyclopterus lumpus L.)

The use of lumpfish (Cyclopterus lumpus) as a cleaner fish to fight sea lice infestation in farmed Atlantic salmon has become increasingly common. Still, tools to increase our knowledge about lumpfish biology are lacking. Here, we successfully established and characterized the first Lumpfish Gill cell line (LG-1). LG-1 are adherent, homogenous and have a flat, stretched-out and almost transparent appearance. Transmission electron microscopy revealed cellular protrusions and desmosome-like structures that, together with their ability to generate a transcellular epithelial/endothelial resistance, suggest an epithelial or endothelial cell type. Furthermore, the cells exert Cytochrome P450 1A activity. LG-1 supported the propagation of several viruses that may lead to severe infectious diseases with high mortalities in fish farming, including viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV). Altogether, our data indicate that the LG-1 cell line originates from an epithelial or endothelial cell type and will be a valuable in vitro research tool to study gill cell function as well as host-pathogen interactions in lumpfish.

Early detection of salmonid alphavirus in seawater from marine farm sites of Atlantic salmon Salmo salar

The traditional strategy for national surveillance of salmonid alphavirus (SAV) infection in Norwegian fish farms relies on a costly, time-consuming, and resource-demanding approach based on the monthly sampling of fish from all marine farms with salmonids. In order to develop an alternative surveillance method, a water filtration method was tested in parallel with the ongoing surveillance program at 7 Norwegian marine farm sites of Atlantic salmon Salmo salar L. with no current suspicion of SAV infection. During the period from May 2019 to January 2020, seawater samples were collected from the top layer water inside all net-pens at these 7 sites. The samples were concentrated for SAV by filtration through an MF-Millipore™ electronegative membrane filter, followed by rinsing with NucliSENS® Lysis Buffer, before RNA extraction and analysis by RT-qPCR. SAV was detected from seawater at an earlier stage compared to traditional sampling methods, at all sites where the fish tested positive for SAV. A significant negative relationship was observed at all sites between the SAV concentration found in seawater samples and the number of days until SAV was detected in the fish. This means that the fewer the SAV particles in the seawater, the more days it took until SAV was detected in the fish samples. Based on this, sampling of seawater every month for the surveillance of SAV has a great potential as an alternative method for early detection of SAV in Atlantic salmon farms.

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

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.

Genetically modified attenuated salmonid alphavirus: A potential strategy for immunization of Atlantic salmon

Pancreas disease (PD) is a serious challenge in European salmonid aquaculture caused by salmonid alphavirus (SAV). In this study, we report the effect of immunization of Atlantic salmon with three attenuated infectious SAV3 strains with targeted mutations in a glycosylation site of the envelope E2 protein and/or in a nuclear localization signal in the capsid protein. In a pilot experiment, it was shown that the mutated viral strains replicated in fish, transmitted to naïve cohabitants and that the transmission had not altered the sequences. In the main experiment, the fish were immunized with the strains and challenged with SAV3 eight weeks after immunization. Immunization resulted in infection both in injected fish and 2 weeks later in the cohabitant fish, followed by a persistent but declining load of the mutated virus variants in the hearts. The immunized fish developed clinical signs and pathology consistent with PD prior to challenge. However, fish injected with the virus mutated in both E2 and capsid showed little clinical signs and had higher average weight gain than the groups immunized with the single mutated variants. The SAV strain used for challenge was not detected in the immunized fish indicating that these fish were protected against superinfection with SAV during the 12 weeks of the experiment.

A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon

Atlantic salmon (Salmo salar) is a major species produced in world aquaculture and an important vertebrate model organism for studying the process of rediploidization following whole genome duplication events (Ss4R, 80 mya). The current Salmo salar transcriptome is largely generated from genome sequence based in silico predictions supported by ESTs and short-read sequencing data. However, recent progress in long-read sequencing technologies now allows for full-length transcript sequencing from single RNA-molecules. This study provides a de novo full-length mRNA transcriptome from liver, head-kidney and gill materials. A pipeline was developed based on Iso-seq sequencing of long-reads on the PacBio platform (HQ reads) followed by error-correction of the HQ reads by short-reads from the Illumina platform. The pipeline successfully processed more than 1.5 million long-reads and more than 900 million short-reads into error-corrected HQ reads. A surprisingly high percentage (32%) represented expressed interspersed repeats, while the remaining were processed into 71 461 full-length mRNAs from 23 071 loci. Each transcript was supported by several single-molecule long-read sequences and at least three short-reads, assuring a high sequence accuracy. On average, each gene was represented by three isoforms. Comparisons to the current Atlantic salmon transcripts in the RefSeq database showed that the long-read transcriptome validated 25% of all known transcripts, while the remaining full-length transcripts were novel isoforms, but few were transcripts from novel genes. A comparison to the current genome assembly indicates that the long-read transcriptome may aid in improving transcript annotation as well as provide long-read linkage information useful for improving the genome assembly. More than 80% of transcripts were assigned GO terms and thousands of transcripts were from genes or splice-variants expressed in an organ-specific manner demonstrating that hybrid error-corrected long-read transcriptomes may be applied to study genes and splice-variants expressed in certain organs or conditions (e.g., challenge materials). In conclusion, this is the single largest contribution of full-length mRNAs in Atlantic salmon. The results will be of great value to salmon genomics research, and the pipeline outlined may be applied to generate additional de novo transcriptomes in Atlantic Salmon or applied for similar projects in other species.

Filtration, concentration and detection of salmonid alphavirus in seawater during a post-smolt salmon (Salmo salar) cohabitant challenge

Currently, the prevalence of salmonid alphavirus (SAV) in Norwegian Atlantic salmon farms is largely surveyed via sacrificing fish and sampling of organ tissue on a monthly basis. However, a more cost-efficient, straightforward, rapid, reliable, reproducible and animal welfare friendly method based on the detection of SAV in water could be considered as an alternative method. In the present study, such a method was developed and optimized through a 6 wk cohabitant challenge trial, using post-smolt Atlantic salmon Salmo salar L challenged with high or low doses of SAV subtype 3 (SAV3). Tank water and tissue samples from cohabitant fish were collected at 16 time points. SAV3 was concentrated from the water by filtration, using either electronegative or electropositive membrane filters, which were subsequently rinsed with one of 4 different buffer solutions. SAV3 was detected first in tank water (7 d post-challenge, DPC), and later in cohabitant fish organ tissue samples (12 DPC). The electronegative filter (MF-Millipore™) and rinsing with NucliSENS® easyMAG® Lysis Buffer presented the best SAV3 recovery. A significant positive correlation was found between SAV3 in the tank water concentrates and the mid-kidney samples. Based on these results, detection of SAV3 in filtrated seawater is believed to have the potential to serve as an alternative method for surveillance of SAV in Atlantic salmon farms.

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)

The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak of Branchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.

Non-Lethal Sequential Individual Monitoring of Viremia in Relation to DNA Vaccination in Fish-Example Using a Salmon Alphavirus DNA Vaccine in Atlantic Salmon Salmo salar

Traditionally, commercial testing for vaccine efficacy has relied on the mass infection of vaccinated and unvaccinated animals and the comparison of mortality prevalence and incidence. For some infection models where disease does not cause mortality this approach to testing vaccine efficacy is not useful. Additionally, in fish experimental studies on vaccine efficacy and immune response the norm is that several individuals are lethally sampled at sequential timepoints, and results are extrapolated to represent the kinetics of immune and disease parameters of an individual fish over the entire experimental infection period. In the present study we developed a new approach to vaccine testing for viremic viruses in fish by following the same individuals over the course of a DNA vaccination and experimental infection through repeated blood collection and analyses. Injectable DNA vaccines are particularly efficient against viral disease in fish. To date, two DNA vaccines have been authorised for use in fish farming, one in Canada against Infectious Haemorrhagic Necrotic virus and more recently one in Europe against Salmon Pancreatic Disease virus (SPDv) subtype 3. In the current study we engineered and used an experimental DNA vaccine against SPDv subtype 1. We measured viremia using a reporter cell line system and demonstrated that the viremia phase was completely extinguished following DNA vaccination. Differences in viremia infection kinetics between fish in the placebo group could be related to subsequent antibody levels in the individual fish, with higher antibody levels at terminal sampling in fish showing earlier viremia peaks. The results indicate that sequential non-lethal sampling can highlight associations between infection traits and immune responses measured at asynchronous timepoints and, can provide biological explanations for variation in data. Similar to results observed for the SPDv subtype 3 DNA vaccine, the SPDv subtype 1 DNA vaccine also induced an interferon type 1 response after vaccination and provided high protection against SPDv under laboratory conditions when fish were challenged at 7 weeks post-vaccination.

The effect of fasting period on swimming performance, blood parameters and stress recovery in Atlantic salmon post smolts

In this study, Atlantic salmon post smolts (~250 g, ~29 cm) were fasted for four weeks at 12 °C in full strength seawater. During this period, the critical swimming speed (U_crit) was measured after 1, 2 and 4 weeks of fasting, as well as in a fed control group. Furthermore, blood samples were taken in each treatment group prior to the swim test, at fatigue, and following 3 h and 24 h of subsequent recovery. Four weeks of fasting gradually reduced the condition factor from 1.03 to 0.89. However, the U_crit remained statistically unaffected at 3.5 body lengths s^-1. Exhaustive exercise stress caused large increases in plasma osmolality, [Cl^-], [Na⁺], [Ca²⁺], [lactate] and [cortisol], while haematocrit and [haemoglobin] also increased. Plasma ions and lactate had increased further after 3 h recovery, and osmolality, [Cl^-] and [Na⁺] were still elevated above control levels after 24 h while other blood parameters were fully recovered. Osmotic disturbances may therefore be considered the most challenging stressor during strenuous exercise in seawater. Only minor effects of fasting period on blood parameters in response to exhaustive exercise were detected, which included slightly higher osmotic disturbances and a repressed response in red blood cell recruitment at fatigue in fasted fish. Furthermore, the 4-week fasting group had a reduced cortisol response following fatigue compared to the other treatment groups. In conclusion, these results show that Atlantic salmon maintain their full swimming capacity as well as their ability to respond and recover from acute stress during an extended period of food deprivation.

Cellular Immune Responses in Rainbow Trout (Onchorhynchus mykiss) Following Vaccination and Challenge Against Salmonid Alphavirus (SAV)

Viral disease outbreaks remain a significant limiting factor for aquaculture. The majority of licensed vaccines used in the industry are administered as oil-adjuvanted formulations carrying inactivated whole pathogens. Cell-mediated immune responses, in particular those based on virus-specific cytotoxic T-cells (CTLs) to conventional inactivated oil-based vaccines, are largely unexplored. As vaccines cannot be optimized against viral pathogens if knowledge of host cellular immune mechanisms remains unknown, in this study we examined fundamental cell-mediated immune responses after vaccination of rainbow trout with an oil-adjuvanted inactivated vaccine against salmonid alphavirus (SAV) and after infection with SAV. A unique in vitro model system was developed to examine MHC class I restricted CTL responses in a clonal line of rainbow trout. The levels of cell-mediated cytotoxicity were compared to pathology, virus load, specific antibody response, changes in immune cell populations, and mRNA expression. Our results hint that different protective mechanisms are being triggered by infection compared to vaccination. While vaccination itself did not cause a strong cytotoxic or humoral response, subsequent challenge of vaccinated fish resulted in significantly stronger and faster specific cytotoxicity, alongside reduced viral titers and pathology. Hence, testing a vaccine on the capacity to induce cell-mediated cytotoxicity will still require a challenge test. Examination of cellular markers additionally indicates that the initial innate response induced by the vaccine could play an important role in steering adaptive mechanisms.

Atlantic salmon kidney (ASK) cells are an effective model to characterise interferon (IFN) and IFN-induced gene expression following salmonid alphavirus infection

Salmonid alphavirus (SAV), the causative agent of pancreas disease, is a serious pathogen of farmed Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Given the economic impact of SAV outbreaks, much effort is focussed upon understanding the fish immune response following infection and the exploitation of this knowledge to reduce disease impact. Herein we examine the utility of the long-term Atlantic salmon kidney (ASK) cell line as a tool to study antiviral responses upon infection with SAV. Following infection with SAV subtype 1 (isolate V4640) we examined the kinetics and magnitude of induction of IFNa, IFN-regulatory factor (IRF) genes IRF1, IRF3, and IRF7b, as well as the antiviral effector Mx by RT-qPCR. SAV-1 non-structural protein (nsp1) transcript levels increased continuously over the experimental period, indicating viral replication, but cytopathic effect (CPE) was not observed. All the immune genes studied showed an increase in transcript levels over the 96-h study period following SAV infection, with strongest induction of Mx. Our data confirm that ASK cells are a suitable model to study the virus-associated immune responses of salmonids and may be a useful tool when assaying the effectiveness of potential prophylactic or antiviral treatments.

Detection of specific Atlantic salmon antibodies against salmonid alphavirus using a bead-based immunoassay

Salmonid alphavirus (SAV) is the etiological cause of pancreas disease (PD) in Atlantic salmon (Salmo salar). Several vaccines against SAV are in use, but PD still cause significant mortality and concern in European aquaculture, raising the need for optimal tools to monitor SAV immunity. To monitor and control the distribution of PD in Norway, all salmonid farms are regularly screened for SAV by RT-qPCR. While the direct detection of SAV is helpful in the early stages of infection, serological methods could bring additional information on acquired SAV immunity in the later stages. Traditionally, SAV antibodies are monitored in neutralization assays, but they are time-consuming and cumbersome, thus alternative assays are warranted. Enzyme-linked immunosorbent assays (ELISAs) have not yet been successfully used for anti-SAV antibody detection in aquaculture. We aimed to develop a bead-based immunoassay for SAV-specific antibodies. By using detergent-treated SAV particles as antigens, we detected SAV-specific antibodies in plasma collected from both a SAV challenge trial and a field outbreak of PD. Increased levels of SAV-specific antibodies were seen after most fish had become negative for viral RNA. The bead-based assay is time saving compared to virus neutralization assays, and suitable for non-lethal testing due to low sample size requirements. We conclude that the bead-based immunoassay for SAV antibody detection is a promising diagnostic tool to complement SAV screening in aquaculture.

Characterization of an alphavirus isolated from a stranded harbor porpoise (Phocoena phocoena) from Alaska

The family Togaviridae comprises several significant human and veterinary mosquito-borne pathogens. Two togaviruses (genus Alphavirus) have been previously identified in association with marine mammals, the southern elephant seal virus (SESV) and Eastern equine encephalitis virus (EEEV) from a fatal captive harbor seal infection. Herein we report the ultrastructural and phylogenomic characterization of a novel marine togavirus, the first isolated from a cetacean, an Alaskan harbor porpoise (Phocoena phocoena) displaying ulcerative dermatitis. A skin sample was processed for virus isolation on Vero.DogSLAMtag cells and cytopathic effects (CPE) were observed on primary isolation approximately 20 days post-infection. Transmission electron microscopy of the infected Vero.DogSLAMtag cells revealed typical alphavirus particles budding from both plasma and vacuolar membranes of infected cells. A next-generation sequencing approach was used to determine the near complete genome of the Alaskan harbor porpoise alphavirus (AHPV). Phylogenetic analysis supported the AHPV as the sister species to the SESV, forming a marine mammal alphavirus clade separate from the recognized alphavirus antigenic complexes. Genetic comparison of the protein coding sequence of the AHPV to other alphaviruses demonstrated amino acid identities ranging from 42.1-67.1%, with the highest identity to the SESV. Based on its genetic divergence, we propose the AHPV represents a novel alphavirus species, pending formal proposal to and ratification by the International Committee on Taxonomy of Viruses. The ecological and genetic characteristics of the AHPV and the SESV also suggest they represent a novel antigenic complex within the genus Alphavirus, which we propose to be named the Marine Mammal Virus Complex. The role of the AHPV in the associated harbor porpoise cutaneous pathology, if any, remains unclear. Further research is needed to determine AHPV's route(s) of transmission and potential vectors, host range, prevalence, and pathogenicity in cetaceans including harbour porpoises.

Mutation of N-glycosylation Sites in Salmonid Alphavirus (SAV) Envelope Proteins Attenuate the Virus in Cell Culture

Salmonid alphavirus (SAV) is the cause of pancreas disease and sleeping disease in farmed salmonid fish in Europe. The spread of these diseases has been difficult to control with biosecurity and current vaccination strategies, and increased understanding of the viral pathogenesis could be beneficial for the development of novel vaccine strategies. N-glycosylation of viral envelope proteins may be crucial for viral virulence and a possible target for its purposed attenuation. In this study, we mutated the N-glycosylation consensus motifs of the E1 and E2 glycoproteins of a SAV3 infectious clone using site-directed mutagenesis. Mutation of the glycosylation motif in E1 gave a complete inactivation of the virus as no viral replication could be detected in cell culture and infectious particles could not be rescued. In contrast, infectious virus particles could be recovered from the SAV3 E2 mutants (E2319Q, E2319A), but not if they were accompanied by lack of N-glycosylation in E1. Compared to the non-mutated infectious clone, the SAV3-E2319Q and SAV3-E2319A recombinant viruses produced less cytopathic effects in cell culture and lower amounts of infectious viral particles. In conclusion, the substitution in the N-linked glycosylation site in E2 attenuated SAV3 in cell culture. The findings could be useful for immunization strategies using live attenuated vaccines and testing in fish will be desirable to study the clone’s properties in vivo.

IgM+ and IgT+ B Cell Traffic to the Heart during SAV Infection in Atlantic Salmon

B cells of teleost fish differentiate in the head kidney, and spleen, and either remain in the lymphatic organs or move to the blood and peripheral tissues. There is limited knowledge about piscine B cell traffic to sites of vaccination and infection and their functional roles at these sites. In this work, we examined the traffic of B cells in Atlantic salmon challenged with salmonid alphavirus (SAV). In situ hybridization (RNAScope) showed increased numbers of immunoglobin (Ig)M+ and IgT+ B cells in the heart in response to SAV challenge, with IgM+ B cells being most abundant. An increase in IgT+ B cells was also evident, indicating a role of IgT+ B cells in nonmucosal tissues and systemic viral infections. After infection, B cells were mainly found in the stratum spongiosum of the cardiac ventricle, colocalizing with virus-infected myocardial-like cells. From sequencing the variable region of IgM in the main target organ (heart) and comparing it with a major lymphatic organ (the spleen), co-occurrence in antibody repertoires indicated a transfer of B cells from the spleen to the heart, as well as earlier recruitment of B cells to the heart in vaccinated fish compared to those that were unvaccinated. Transcriptome analyses performed at 21 days post-challenge suggested higher expression of multiple mediators of inflammation and lymphocyte-specific genes in unvaccinated compared to vaccinated fish, in parallel with a massive suppression of genes involved in heart contraction, metabolism, and development of tissue. The adaptive responses to SAV in vaccinated salmon appeared to alleviate the disease. Altogether, these results suggest that migration of B cells from lymphatic organs to sites of infection is an important part of the adaptive immune response of Atlantic salmon to SAV.

Polarized Trout Epithelial Cells Regulate Transepithelial Electrical Resistance, Gene Expression, and the Phosphoproteome in Response to Viral Infection

The burden of disease is a major challenge in aquaculture production. The fish gill characterized with a large surface area and short route to the bloodstream is a major environmental interface and a significant portal of entry for pathogens. To investigate gill responses to viral infection the salmonid gill cell line RTgill-W1 was stimulated with synthetic dsRNA and the salmonid alphavirus subtype 2 (SAV-2). Epithelial integrity in polarized cells can be measured as transepithelial electrical resistance (TEER) which is defined as the electrical resistance across a cell monolayer. TEER is a widely accepted quantitative measure of cellular integrity of a cell monolayer. TEER increased immediately after stimulation with the synthetic dsRNA, polyinosinic:polycytidylic acid (poly(I:C)). In parallel, tight junction and gene expression of innate immune activation markers was modulated in response to poly(I:C). The SAV-2 virus was found to replicate at a low level in RTgill-W1 cells where TEER was disturbed at an early stage of infection, however, gene expression related to tight junction regulation was not modulated. A strong poly(I:C)-driven antiviral response was observed including increases of Rig-like receptors (RLRs) and interferon stimulating genes (ISGs) mRNAs. At the level of signal transduction, poly(I:C) stimulation was accompanied by the phosphorylation of 671 proteins, of which 390 were activated solely in response to the presence of poly(I:C). According to motif analysis, kinases in this group included MAPKs, Ca2+/calmodulin-dependent kinase (CaMK) and cAMP-dependent protein kinase (PKA), all reported to be activated in response to viral infection in mammals. Results also highlighted an activation of the cytoskeletal organization that could be mediated by members of the integrin family. While further work is needed to validate these results, our data indicate that salmonid gill epithelia has the ability to mount a significant response to viral infection which might be important in disease progression. In vitro cell culture can facilitate both a deeper understanding of the anti-viral response in fish and open novel therapeutic avenues for fish health management in aquaculture.

Agua Salud alphavirus defines a novel lineage of insect-specific alphaviruses discovered in the New World

The genus Alphavirus harbours mostly insect-transmitted viruses that cause severe disease in humans, livestock and wildlife. Thus far, only three alphaviruses with a host range restricted to insects have been found in mosquitoes from the Old World, namely Eilat virus (EILV), Taï Forest alphavirus (TALV) and Mwinilunga alphavirus (MWAV). In this study, we found a novel alphavirus in one Culex declarator mosquito sampled in Panama. The virus was isolated in C6/36 mosquito cells, and full genome sequencing revealed an 11 468 nt long genome with maximum pairwise nucleotide identity of 62.7 % to Sindbis virus. Phylogenetic analyses placed the virus as a solitary deep rooting lineage in a basal relationship to the Western equine encephalitis antigenic complex and to the clade comprising EILV, TALV and MWAV, indicating the detection of a novel alphavirus, tentatively named Agua Salud alphavirus (ASALV). No growth of ASALV was detected in vertebrate cell lines, including cell lines derived from ectothermic animals, and replication of ASALV was strongly impaired above 31 °C, suggesting that ASALV represents the first insect-restricted alphavirus of the New World.

Identification of genetic loci associated with higher resistance to pancreas disease (PD) in Atlantic salmon (Salmo salar L.)

Background

Pancreas disease (PD) is a contagious disease caused by salmonid alphavirus (SAV) with significant economic and welfare impacts on salmon farming. Previous work has shown that higher resistance against PD has underlying additive genetic components and can potentially be improved through selective breeding. To better understand the genetic basis of PD resistance in Atlantic salmon, we challenged 4506 smolts from 296 families of the SalmoBreed strain. Fish were challenged through intraperitoneal injection with the most virulent form of the virus found in Norway (i.e., SAV3). Mortalities were recorded, and more than 900 fish were further genotyped on a 55 K SNP array.

Results

The estimated heritability for PD resistance was 0.41 ± 0.017. The genetic markers on two chromosomes, ssa03 and ssa07, showed significant associations with higher disease resistance. Collectively, markers on these two QTL regions explained about 60% of the additive genetic variance. We also sequenced and compared the cardiac transcriptomics of moribund fish and animals that survived the challenge with a focus on candidate genes within the chromosomal segments harbouring QTL. Approximately 200 genes, within the QTL regions, were found to be differentially expressed. Of particular interest, we identified various components of immunoglobulin-heavy-chain locus B (IGH-B) on ssa03 and immunoglobulin-light-chain on ssa07 with markedly higher levels of transcription in the resistant animals. These genes are closely linked to the most strongly QTL associated SNPs, making them likely candidates for further investigation.

Conclusions

The findings presented here provide supporting evidence that breeding is an efficient tool for increasing PD resistance in Atlantic salmon populations. The estimated heritability is one of the largest reported for any disease resistance in this species, where the majority of the genetic variation is explained by two major QTL. The transcriptomic analysis has revealed the activation of essential components of the innate and the adaptive immune responses following infection with SAV3. Furthermore, the complementation of the genomic with the transcriptomic data has highlighted the possible critical role of the immunoglobulin loci in combating PD virus.

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

Understanding the dynamics of pathogen transfer in aquaculture systems is essential to manage and mitigate disease outbreaks. The goal of this study was to understand recent transmission dynamics of salmonid alphavirus (SAV) in Norway. SAV causes significant economic impacts on farmed salmonids in European aquaculture. SAV is classified into six subtypes, with Norway having ongoing epidemics of SAV subtypes 2 and 3. These two viral subtypes are present in largely distinct geographic regions of Norway, with SAV2 present in Trondelag, SAV3 in Rogaland, Sogn og Fjordane, and Hordaland, and Møre og Romsdal having outbreaks of both subtypes. To determine likely transmission routes of Norwegian SAV an established Nanopore amplicon sequencing approach was used in the current study. After confirming the accuracy of this approach for distinguishing subtype level co-infections of SAV2 and SAV3, a hypothetical possibility in regions of neighboring epidemics, twenty-four SAV3 genomes were sequenced to characterize the current genetic diversity of SAV3 in Norwegian aquaculture. Sequencing was performed on naturally infected heart tissues originating from a range of geographic locations sampled between 2016 and 2019. Phylogenetic analyses revealed that the currently active SAV3 strains sampled comprise several distinct lineages sharing an ancestor that existed ∼15 years ago (95% HPD, 12.51-17.7 years) and likely in Hordaland. At least five of these lineages have not shared a common ancestor for 7.85 years (95% HPD, 5.39-10.96 years) or more. Furthermore, the ancestor of the strains that were sampled outside of Hordaland (Sogn of Fjordane and Rogaland) existed less than 8 years ago, indicating a lack of long-term viral reservoirs in these counties. This evident lack of geographically distinct subclades is compatible with a source-sink transmission dynamic explaining the long-term movements of SAV around Norway. Such anthropogenic transport of the virus indicates that at least for sink counties, biosecurity strategies might be effective in mitigating the ongoing SAV epidemic. Finally, genomic analyses of SAV sequences were performed, offering novel insights into the prevalence of SAV genomes containing defective deletions. Overall, this study improves our understanding of the recent transmission dynamics and biology of the SAV epidemic affecting Norwegian aquaculture.

Field Evaluation of Diagnostic Test Sensitivity and Specificity for Salmonid Alphavirus (SAV) Infection and Pancreas Disease (PD) in Farmed Atlantic salmon (Salmo salar L.) in Norway Using Bayesian Latent Class Analysis

Salmonid alphavirus (SAV) is the OIE-listed, viral cause of pancreas disease (PD) in farmed Atlantic salmon. SAV is routinely detected by PCR–methods while typical histopathological lesions are additionally used to confirm the diagnosis. Field evaluation of diagnostic test performance is essential to ensure confidence in a test's ability to predict the infection or disease status of a target animal. For most tests used in aquaculture, characteristics like sensitivity (Se) and specificity (Sp) at the analytical level may be known. Few tests are, however, evaluated at the diagnostic level according to the OIE standard. In the present work, we estimated diagnostic test sensitivity (DSe) and diagnostic test specificity (DSp) for five laboratory tests used for SAV detection. As there is no gold standard, the study was designed using Bayesian latent class analysis. Real-time RT-PCR, cell culture, histopathology, virus neutralization test, and immunohistochemistry were compared using samples taken from three different farmed Atlantic salmon populations with different infection status; one population regarded negative, one in an early stage of infection, and one in a later stage of infection. The average fish weight in the three populations was 2.0, 1.6, and 1.5 kg, respectively. The DSe and DSp of real-time RT-PCR is of particular interest due to its common use as a screening tool. The method showed high DSe (≥0.977) and moderate DSp (0.831) in all 3-populations models. The results further suggest that a follow-up test of serum samples in real-time RT-PCR negative populations may be prudent in cases where epidemiological information suggest a high risk of infection and where a false negative result is of high consequence. This study underlines the need to choose a test appropriate for the purpose of the testing. In the case of a weak positive PCR-result, a follow-up test should be conducted to verify the presence of SAV. Cell culture showed high DSe and DSp and may be used to verify viral presence.

Identification of a novel alphavirus related to the encephalitis complexes circulating in southern Brazil

In early 2017, an outbreak caused by an unknown and supposedly viral agent in the Marilena region of southern Brazil was investigated. Since the etiological agent causing the outbreak was not identified from human samples, mosquitoes from this region were collected. Three out of 121 mosquito pools collected from the region tested positive for alphavirus in molecular tests. Next generation sequencing results revealed the presence of a novel alphavirus, tentatively named here as Caainguá virus (CAAV). DNA barcoding analyses indicated that different species of Culex are hosts for CAAV. This new virus was basal to the New World encephalitic alphaviruses in a comprehensive and robust phylogenetic approach using complete genomes. Viral particles were observed in the cytosol and inside of intracellular compartments of cells in mosquito-derived cell cultures. Despite being noninfectious in vertebrate derived cell cultures, primary culturing of CAAV in human mononuclear cells suggests monocytes and lymphocytes as CAAV targets. However, the epidemiological link of CAAV on the human outbreak should be further explored.

Pancreas disease caused by Salmonid alphavirus subtype 2 reduces growth and feed conversion in farmed Atlantic salmon

Pancreas disease (PD), caused by several subtypes of salmonid alphavirus (SAV), is associated with significant economic losses in European salmonid aquaculture. In this retrospective cohort study, we investigate the impact of PD caused by SAV subtype 2 (SAV2) on growth, feed conversion, and mortality in farmed Atlantic salmon (Salmo salar L.). The study was based on harvest data from a large salmon farming company operating in the SAV2 endemic area of Norway. Mixed-effect regression analyses showed a severe impact on both growth and feed conversion when PD appeared late in the production cycle. In a scenario with fixed slaughter time the estimated impact corresponded to a growth reduction of 0.7 kg and 0.07 points increase in feed conversion ratio. No effect on mortality was observed in this data set. In conclusion, the most important consequences of PD caused by SAV2 infection is reduced growth and feed conversion in large Atlantic salmon. The lack of effect on mortality in this study may be due to other factors overshadowing the impact of PD.

Antiviral defense in salmonids - Mission made possible?

Viral diseases represent one of the major threats for salmonid aquaculture. Survival from viral infections are highly dependent on host innate antiviral immune defense, where interferons are of crucial importance. Neutralizing antibodies and T cell effector mechanisms mediate long-term antiviral protection. Despite an immune cell repertoire comparable to higher vertebrates, farmed fish often fail to mount optimal antiviral protection. In the quest to multiply and spread, viruses utilize a variety of strategies to evade or escape the host immune system. Understanding the specific interplay between viruses and host immunity at depth is crucial for developing successful vaccination and treatment strategies in mammals. However, this knowledge base is still limited for pathogenic fish viruses. Here, we have focused on five RNA viruses with major impact on salmonid aquaculture: Salmonid alphavirus, Infectious salmon anemia virus, Infectious pancreatic necrosis virus, Piscine orthoreovirus and Piscine myocarditis virus. This review explore the protective immune responses that salmonids mount to these viruses and the existing knowledge on how the viruses counteract and/or bypass the immune response, including their IFN antagonizing effects and their mechanisms to establish persisting infections.

Effect of pancreas disease caused by SAV 2 on protein and fat digestion in Atlantic salmon

Salmonid alphavirus (SAV) causes pancreas disease (PD) in farmed Atlantic salmon (Salmo salar L.), and exocrine pancreas tissue is a primary target of the virus. Digestive enzymes secreted by the exocrine pancreas break down macromolecules in feed into smaller molecules that can be absorbed. The effect of SAV infection on digestion has been poorly studied. In this study, longitudinal observations of PD outbreaks caused by SAV subtype 2 (SAV2) in Atlantic salmon at two commercial sea sites were performed. The development of PD was assessed by measurement of SAV2 RNA load and evaluation of histopathological lesions typical of PD. Reduced digestion of both protein and fat co-varied with the severity of PD lesions and viral load. Also, the study found that during a PD outbreak, the pen population comprise several subpopulations, with different likelihoods of being sampled. The body length of sampled fish deviated from the expected increase or steady state over time, and the infection status in sampled fish deviated from the expected course of infection in the population. Both conditions indicate that disease status of the individual fish influenced the likelihood of being sampled, which may cause sampling bias in population studies.

Increased dietary protein-to-lipid ratio improves survival during naturally occurring pancreas disease in Atlantic salmon, Salmo salar L

This study demonstrated that increased dietary protein-to-lipid ratio (P/L-ratio) improved survival of farmed Atlantic salmon naturally affected by pancreas disease (PD). In addition to diet, body weight (BW) and delousing mortality prior to the PD outbreak also contributed significantly (p < 0.05) to explain the observed variation in PD-associated mortality. Subsequent to the PD outbreak, large amount of fish failed to grow and caused thin fish with poor condition (runts). At the end of the trial, significantly (p < 0.05) lower amounts of runt fish and increased amount of superior graded fish where detected among fish fed increased P/L-ratio and within the fish with the largest BWs prior to PD. Diet, BW and delousing mortality contributed significantly (p < 0.05) to explain the variation in the amount of superior graded fish, whereas BW and diet explained the variation in the amount of runt fish. A significant (p < 0.01) negative linear relationship was observed between the amount of superior graded fish and the total mortality, whereas a positive linear relationship was detected between percentage of fillets with melanin and the total mortality. Thus, increased dietary P/L-ratio seem to reduce the mortality and impaired slaughter quality associated with PD.

Isolation of salmonid alphavirus subtype 6 from wild-caught ballan wrasse, Labrus bergylta (Ascanius)

The use of cleaner fish as a biological control for sea lice in Atlantic salmon aquaculture has increased in recent years. Wild-caught wrasse are commonly used as cleaner fish in Europe. In Ireland, samples of wrasse from each fishing area are screened for potential pathogens prior to their deployment into sea cages. Salmonid alphavirus was isolated from a pooled sample of ballan wrasse, showing no signs of disease, caught from the NW of Ireland. Partial sequencing of the E2 and nsP3 genes showed that it was closely related to the previously reported SAV subtype 6. This represents only the second isolation of this subtype and the first from a wild fish species, namely ballan wrasse.

Atlantic salmon post-smolts adapted for a longer time to seawater develop an effective humoral and cellular immune response against Salmonid alphavirus

Salmonid alphavirus (SAV) causes pancreas disease (PD) in Atlantic salmon (Salmo salar L.) and disease outbreaks are mainly detected after seawater transfer. The influence of the smoltification process on the immune responses, specifically the adaptive response of Atlantic salmon after SAV infection, is not fully understood. In this study, Atlantic salmon post-smolts were infected by either bath immersion (BI) or intramuscular injection (IM) with SAV subtype 3, 2 weeks (Phase A) or 9 weeks (Phase B) after seawater transfer. The transcript levels of genes related to cellular, humoral and inflammatory responses were evaluated on head kidney samples collected at 3, 7, 14, 21, and 28 days post-infection (dpi). Corresponding negative control groups (CT) were established accordingly. Significant differences were found between both phases and between the IM and BI groups. The anti-inflammatory cytokine IL-10 was up-regulated in Phase A at a higher level than in Phase B. High mRNA levels of the genes RIG-1, SOCS1 and STAT1 were observed in all groups except the BI-B group (BI-Phase B). Moreover, the IM-B group showed a higher regulation of genes related to cellular responses, such as CD40, MHCII, and IL-15, that indicated the activation of a strong cell-mediated immune response. CD40 mRNA levels were elevated one week earlier in the BI-B group than in the BI-A group (BI-Phase A). A significant up-regulation of IgM and IgT genes was seen in both IM groups, but the presence of neutralizing antibodies to SAV was detected only in Phase B fish at 21 and 28 dpi. In addition, we found differences in the basal levels of some of the analysed genes between non-infected control groups of both phases. Findings suggest that Atlantic salmon post-smolts adapted for a longer time to seawater before they come into contact with SAV, developed a stronger humoral and cell-mediated immune response during a SAV infection.

First confirmation of salmonid alphavirus infection in Arctic char Salvelinus alpinus and in Austria

To date, sleeping disease (SD) caused by salmonid alphavirus 2 (SAV 2) has been reported in freshwater rainbow trout Oncorhynchus mykiss and Atlantic salmon Salmo salar. This study describes for the first time the occurrence of SD in farm-reared Arctic char Salvelinus alpinus and the occurrence of SAV in Austria. Clinical symptoms were indicative of the disease, and the diagnosis was confirmed by histopathology, infectivity in first passages of CHSE-214 cells and PCR. The phylogenetic analysis of the amplified SAV-nonstructural protein-3 (nsP3) fragment revealed the affiliation to the SAV 2 genotype.

Genetic control of alphavirus pathogenesis

Alphaviruses, members of the positive-sense, single-stranded RNA virus family Togaviridae, represent a re-emerging public health concern worldwide as mosquito vectors expand into new geographic ranges. Members of the alphavirus genus tend to induce clinical disease characterized by rash, arthralgia, and arthritis (chikungunya virus, Ross River virus, and Semliki Forest virus) or encephalomyelitis (eastern equine encephalitis virus, western equine encephalitis virus, and Venezuelan equine encephalitis virus), though some patients who recover from the initial acute illness may develop long-term sequelae, regardless of the specific infecting virus. Studies examining the natural disease course in humans and experimental infection in cell culture and animal models reveal that host genetics play a major role in influencing susceptibility to infection and severity of clinical disease. Genome-wide genetic screens, including loss of function screens, microarrays, RNA-sequencing, and candidate gene studies, have further elucidated the role host genetics play in the response to virus infection, with the immune response being found in particular to majorly influence the outcome. This review describes the current knowledge of the mechanisms by which host genetic factors influence alphavirus pathogenesis and discusses emerging technologies that are poised to increase our understanding of the complex interplay between viral and host genetics on disease susceptibility and clinical outcome.

Genetic effects of fatty acid composition in muscle of Atlantic salmon

BACKGROUND

The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in their filets. Previous studies showed the potential of selective breeding to increase n-3 LC-PUFA levels in salmon tissues, but knowledge on the genetic parameters for individual muscle fatty acids (FA) and their relationships with other traits is still lacking. Thus, we estimated genetic parameters for muscle content of individual FA, and their relationships with lipid deposition traits, muscle pigmentation, sea lice and pancreas disease in slaughter-sized Atlantic salmon. Our aim was to evaluate the selection potential for increased n-3 LC-PUFA content and provide insight into FA metabolism in Atlantic salmon muscle.

RESULTS

Among the n-3 PUFA, proportional contents of alpha-linolenic acid (ALA; 18:3n-3) and DHA had the highest heritability (0.26) and EPA the lowest (0.09). Genetic correlations of EPA and DHA proportions with muscle fat differed considerably, 0.60 and 0.01, respectively. The genetic correlation of DHA proportion with visceral fat was positive and high (0.61), whereas that of EPA proportion with lice density was negative. FA that are in close proximity along the bioconversion pathway showed positive correlations with each other, whereas the start (ALA) and end-point (DHA) of the pathway were negatively correlated (- 0.28), indicating active bioconversion of ALA to DHA in the muscle of fish fed high FO-diet.

CONCLUSIONS

Since contents of individual FA in salmon muscle show additive genetic variation, changing FA composition by selective breeding is possible. Taken together, our results show that the heritabilities of individual n-3 LC-PUFA and their genetic correlations with other traits vary, which indicates that they play different roles in muscle lipid metabolism, and that proportional muscle contents of EPA and DHA are linked to body fat deposition. Thus, different selection strategies can be applied in order to increase the content of healthy omega-3 FAin the salmon muscle. We recommend selection for the proportion of EPA + DHA in the muscle because they are both essential FA and because such selection has no clear detrimental effects on other traits.

Salmonid Alphavirus (SAV)

Salmonid alphavirus (SAV), genus Alphavirus, family Togaviridae, is a single-stranded RNA virus affecting Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). It is known to be responsible for pancreas disease (PD) and sleeping disease (SD) which are increasing problems, causing high fish mortality and economic losses in the European aquaculture industry. Pancreas disease was first described in Atlantic salmon in Scotland in 1976 and a similar disease caused by the closely related sleeping disease virus was first described in rainbow trout in France. There have also been reports of salmonid alphavirus infections from other European countries, including Ireland, England, Norway, Germany, Italy, and Spain. Salmonid alphaviruses have been classified into six subtypes (SAV1–6). SAV1 and SAV4–6 cause pancreas disease in Atlantic salmon in Ireland or Scotland, SAV2 is the causative agent of sleeping disease in rainbow trout, and SAV3 has been detected in Atlantic salmon in Norway. The aim of this paper was to summarise current knowledge of infections caused by salmonid alphavirus and diagnostic methods including the newest techniques, and to briefly describe prevention from SAV infections by vaccination.

The role of type I interferons in innate and adaptive immunity against viruses in Atlantic salmon

Type I IFNs (IFN-I) are cytokines, which play a crucial role in innate and adaptive immunity against viruses of vertebrates. In essence, IFN-I are induced and secreted upon host cell recognition of viral nucleic acids and protect other cells against infection by inducing antiviral proteins. Atlantic salmon possesses an extraordinary repertoire of IFN-I genes encompassing at least six different classes (IFNa, IFNb, IFNc, IFNd, IFNe and IFNf) most of which are encoded by several genes. This review describes recent research on the functions of salmon IFNa, IFNb, IFNc and IFNd. As in mammals, expression of different salmon IFN-I in response to virus infection is dependent on their promoters, properties of the virus and the cell's expression of nucleic acid receptors and interferon regulatory factors (IRFs). While IFNa mainly display local antiviral activity, IFNb and IFNc show systemic antiviral activity. In addition, salmon appears to possess several IFN-I receptors, which show selectivity in binding different IFN-I. This complexity in IFN-I and receptors allows for a large variation in functions of the salmon IFN-I. Studies with intramuscular injection of IFN expression plasmids have recently provided surprising results, which may be of relevance for application of IFN-I in prophylaxis against virus infection. Firstly, injection of IFNc plasmid protected salmon presmolts against virus infection for at least 10 weeks. Secondly, IFN plasmids showed potent adjuvant activity when injected together with a DNA vaccine against infectious salmon anemia virus (ISAV).

The Regulation of Translation in Alphavirus-Infected Cells

Sindbis virus (SINV) contains an RNA genome of positive polarity with two open reading frames (ORFs). The first ORF is translated from the genomic RNA (gRNA), rendering the viral non-structural proteins, whereas the second ORF is translated from a subgenomic mRNA (sgRNA), which directs the synthesis of viral structural proteins. SINV infection strongly inhibits host cell translation through a variety of different mechanisms, including the phosphorylation of the eukaryotic initiation factor eIF2α and the redistribution of cellular proteins from the nucleus to the cytoplasm. A number of motifs have been identified in SINV sgRNA, including a hairpin downstream of the AUG initiation codon, which is involved in the translatability of the viral sgRNA when eIF2 is inactivated. Moreover, a 3′-UTR motif containing three stem-loop structures is involved in the enhancement of translation in insect cells, but not in mammalian cells. Accordingly, SINV sgRNA has evolved several structures to efficiently compete for the cellular translational machinery. Mechanistically, sgRNA translation involves scanning of the 5′-UTR following a non-canonical mode and without the requirement for several initiation factors. Indeed, sgRNA-directed polypeptide synthesis occurs even after eIF4G cleavage or inactivation of eIF4A by selective inhibitors. Remarkably, eIF2α phosphorylation does not hamper sgRNA translation during the late phase of SINV infection. SINV sgRNA thus constitutes a unique model of a capped viral mRNA that is efficiently translated in the absence of several canonical initiation factors. The present review will mainly focus in the non-canonical mechanism of translation of SINV sgRNA.

Molecular testing of adult Pacific salmon and trout (Oncorhynchus spp.) for several RNA viruses demonstrates widespread distribution of piscine orthoreovirus in Alaska and Washington

This research was initiated in conjunction with a systematic, multiagency surveillance effort in the United States (U.S.) in response to reported findings of infectious salmon anaemia virus (ISAV) RNA in British Columbia, Canada. In the systematic surveillance study reported in a companion paper, tissues from various salmonids taken from Washington and Alaska were surveyed for ISAV RNA using the U.S.-approved diagnostic method, and samples were released for use in this present study only after testing negative. Here, we tested a subset of these samples for ISAV RNA with three additional published molecular assays, as well as for RNA from salmonid alphavirus (SAV), piscine myocarditis virus (PMCV) and piscine orthoreovirus (PRV). All samples (n = 2,252; 121 stock cohorts) tested negative for RNA from ISAV, PMCV, and SAV. In contrast, there were 25 stock cohorts from Washington and Alaska that had one or more individuals test positive for PRV RNA; prevalence within stocks varied and ranged from 2% to 73%. The overall prevalence of PRV RNA-positive individuals across the study was 3.4% (77 of 2,252 fish tested). Findings of PRV RNA were most common in coho (Oncorhynchus kisutch Walbaum) and Chinook (O. tshawytscha Walbaum) salmon.

Cardiomyopathy syndrome in Atlantic salmon Salmo salar L.: A review of the current state of knowledge

Cardiomyopathy syndrome (CMS) is a severe cardiac disease affecting Atlantic salmon Salmo salar L. The disease was first recognized in farmed Atlantic salmon in Norway in 1985 and subsequently in farmed salmon in the Faroe Islands, Scotland and Ireland. CMS has also been described in wild Atlantic salmon in Norway. The demonstration of CMS as a transmissible disease in 2009, and the subsequent detection and initial characterization of piscine myocarditis virus (PMCV) in 2010 and 2011 were significant discoveries that gave new impetus to the CMS research. In Norway, CMS usually causes mortality in large salmon in ongrowing and broodfish farms, resulting in reduced fish welfare, significant management-related challenges and substantial economic losses. The disease thus has a significant impact on the Atlantic salmon farming industry. There is a need to gain further basic knowledge about the virus, the disease and its epidemiology, but also applied knowledge from the industry to enable the generation and implementation of effective prevention and control measures. This review summarizes the currently available, scientific information on CMS and PMCV with special focus on epidemiology and factors influencing the development of CMS.