Risk factors for pancreas disease (PD) outbreaks in farmed Atlantic salmon and rainbow trout in Norway during 2003–2007

Effects of regional coordination of salmon louse control in reducing negative impacts of salmonid aquaculture on wild salmonids

Parasitic salmon lice (Lepeophtheirus salmonis) are a constraint to the sustainable growth of salmonids in open net pens, and this issue has caused production to level off in recent years in the most aquaculture-intensive areas of Norway. The maximum allowed biomass at a regional level is regulated by using the so-called "traffic light" system, where salmon louse-induced mortality of migrating wild salmon post-smolts is evaluated against set targets. As a case study, we have investigated how a specific aquaculture-intensive area can reduce its louse levels sufficiently to achieve a low impact on wild salmon. Analyses of the output from a virtual post-smolt model that uses data on the reported number of salmon lice in fish farms as key input data and estimates the salmon louse-induced mortality of wild out-migrating Atlantic salmon post-smolts, suggested that female louse abundance on the local farms must be halved in spring to reach the goal implied by the traffic light system. The outcome of a modelling scenario simulating a proposed new plan for coordinated production and fallowing proved beneficial, with an overall reduction in louse infestations and treatment efforts. The interannual variability in louse abundance in spring, however, increased for this scenario, implying unacceptably high louse abundance when many farms were in their second production year. We then combined the scenario with coordinated production with other louse control measures. Only measures that reduced the density of farmed salmonids in open cages in the study area resulted in reductions in salmon louse infestations to acceptable levels. This could be achieved either by stocking with larger fish to reduce exposure time or by reducing fish numbers, e.g. by producing in closed units.

Most of the escaped farmed salmon entering a river during a 5-year period were infected with one or more viruses

Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses. Overall prevalences were: 75.7% for piscine orthoreovirus (PRV-1), 43.6% for salmonid alphavirus (SAV), 31.2% for piscine myocarditis virus (PMCV), 1.2% for infectious pancreatic necrosis virus (IPNV) and 0.4% for salmon anaemia virus (ISAV). A significantly higher prevalence of PMCV infection was observed in immature compared to mature individuals. The prevalence of both SAV and PMCV infections was higher in fish determined by fatty acid profiling to be 'recent' as opposed to 'early' escapees that had been in the wild for a longer period of time. This is the first study to establish a time-series of viral infection status of escapees entering a river with a native salmon population. Our results demonstrate that farmed escapees represent a continuous source of infectious agents which could potentially be transmitted to wild fish populations.

Effect of pancreas disease vaccines on infection levels and virus transmission in Atlantic salmon (Salmo salar) challenged with salmonid alphavirus, genotype 2

Salmonid alphavirus (SAV) causes pancreas disease (PD), which negatively impacts farmed Atlantic salmon. In this study, fish were vaccinated with a DNA-PD vaccine (DNA-PD) and an oil-adjuvanted, inactivated whole virus PD vaccine (Oil-PD). Controls were two non-PD vaccinated groups. Fish were kept in one tank and challenged by cohabitation with SAV genotype 2 in seawater. Protection against infection and mortality was assessed for 84 days (Efficacy study). Nineteen days post challenge (dpc), subgroups of fish from all treatment groups were transferred to separate tanks and cohabited with naïve fish (Transmission study 1) or fish vaccinated with a homologous vaccine (Transmission study 2), to evaluate virus transmission for 26 days (47 dpc). Viremia, heart RT-qPCR and histopathological scoring of key organs affected by PD were used to measure infection levels. RT-droplet digital PCR quantified shedding of SAV into water for transmission studies. The Efficacy study showed that PD associated growth-loss was significantly lower and clearance of SAV2 RNA significantly higher in the PD-DNA group compared to the other groups. The PD-DNA group had milder lesions in the heart and muscle. Cumulative mortality post challenge was low and not different between groups, but the DNA-PD group had delayed time-to-death. In Transmission study 1, the lowest water levels of SAV RNA were measured in the tanks containing the DNA-PD group at 21 and 34 dpc. Despite this, and irrespective of the treatment group, SAV2 was effectively transmitted to the naïve fish during 26-day cohabitation. At 47 dpc, the SAV RNA concentrations in the water were lower in all tanks compared to 34 dpc. In Transmission study 2, none of the DNA-PD immunized cohabitants residing with DNA-PD-vaccinated, pre-challenged fish got infected. In contrast, Oil-PD immunized cohabitants residing with Oil-PD-vaccinated, pre-challenged fish, showed infection levels similar to the naïve cohabitants in Transmission study 1. The results demonstrate that the DNA-PD vaccine may curb the spread of SAV infection as the DNA-PD vaccinated, SAV2 exposed fish, did not spread the infection to cohabiting DNA-PD vaccinated fish. This signifies that herd immunity may be achieved by the DNA-PD vaccine, a valuable tool to control the PD epizootic in farmed Atlantic salmon.

On the prediction of SAV transmission among Norwegian aquaculture sites

Pancreas Disease (PD) is a viral disease that affects Atlantic salmon (Salmo salar) in Norwegian, Scottish and Irish aquaculture. It is caused by salmonid alphavirus (SAV) and represents a significant problem in salmonid farming. Infection with SAV leads to reduced growth, mortality, product downgrading, and has a significant financial impact for the farms. The overall aim of this study is to evaluate the effect of various factors on the transmission of SAV and to create a predictive model capable of providing an early warning system for salmon farms within the Norwegian waters. Using a combination of publicly available databases, specifically BarentsWatch, and privately held PCR analyses a feature set consisting of 11 unique features was created based on the input parameters of the databases. An ensemble model was developed based on this feature set using XG-Boost, Ada-Boost, Random Forest and a Multilayer Perceptron. It was possible to successfully predict SAV transmission with 94.4% accuracy. Moreover, it was possible to predict SAV transmission 8 weeks in advance of a 'PD registration' at individual aquaculture salmon farming sites. Important predictors included well boat movement, environmental factors, proximity to sites with a 'PD registration' and seasonality.

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.

Infectious Salmon Anemia Virus Shedding from Infected Atlantic Salmon (Salmo salar L.)-Application of a Droplet Digital PCR Assay for Virus Quantification in Seawater

Infectious salmon anemia virus (ISAV) infection is currently detected by fish sampling for PCR and immunohistochemistry analysis. As an alternative to sampling fish, we evaluated two different membrane filters in combination with four buffers for elution, concentration, and detection of ISAV in seawater, during a bath challenge of Atlantic salmon (Salmo salar L.) post-smolts with high and low concentrations of ISAV. Transmission of ISAV in the bath challenge was confirmed by a high mortality, clinical signs associated with ISA disease, and detection of ISAV RNA in organ tissues and seawater samples. The electronegatively charged filter, combined with lysis buffer, gave significantly higher ISAV RNA detection by droplet digital PCR from seawater (5.6 × 10⁴ ISAV RNA copies/L; p < 0.001). Viral shedding in seawater was first detected at two days post-challenge and peaked on day 11 post-challenge, one day before mortalities started in fish challenged with high dose ISAV, demonstrating that a large viral shedding event occurs before death. These data provide important information for ISAV shedding that is relevant for the development of improved surveillance tools based on water samples, transmission models, and management of ISA.

Challenges and Solutions to Viral Diseases of Finfish in Marine Aquaculture

Aquaculture is the fastest food-producing sector in the world, accounting for one-third of global food production. As is the case with all intensive farming systems, increase in infectious diseases has adversely impacted the growth of marine fish farming worldwide. Viral diseases cause high economic losses in marine aquaculture. We provide an overview of the major challenges limiting the control and prevention of viral diseases in marine fish farming, as well as highlight potential solutions. The major challenges include increase in the number of emerging viral diseases, wild reservoirs, migratory species, anthropogenic activities, limitations in diagnostic tools and expertise, transportation of virus contaminated ballast water, and international trade. The proposed solutions to these problems include developing biosecurity policies at global and national levels, implementation of biosecurity measures, vaccine development, use of antiviral drugs and probiotics to combat viral infections, selective breeding of disease-resistant fish, use of improved diagnostic tools, disease surveillance, as well as promoting the use of good husbandry and management practices. A multifaceted approach combining several control strategies would provide more effective long-lasting solutions to reduction in viral infections in marine aquaculture than using a single disease control approach like vaccination alone.

Quantitative trait loci and genes associated with salmonid alphavirus load in Atlantic salmon: implications for pancreas disease resistance and tolerance

Salmonid alphavirus infection results in pancreas disease causing severe economic losses for Atlantic salmon aquaculture. Knowledge about genes and pathways contributing to resistance is limited. A 54 K SNP panel was used to genotype 10 full-sibling families each consisting of ~ 110 offspring challenged with salmonid alphavirus subtype 3. Relative heart viral load was assessed at 4- and 10-weeks post-infection using quantitative PCR. A moderate genomic heritability of viral load at 4 weeks (0.15–0.21) and a high positive correlation with survival (0.91–0.98) were detected. Positions of QTL detected on chromosome 3 matched those for survival detected by other studies. The SNP of highest significance occurred in the 3′ untranslated region of gig1, a fish-specific antiviral effector. Locus B of immunoglobulin heavy chain mapped to an area containing multiple SNPs with genome-wide association. Heart mRNA-seq comparing parr from families with high- versus low-genomic breeding value, and matching sample genotypes for SNPs, identified two eQTL for salmonid alphavirus load. Immune genes associated with trans-eQTL were numerous and spread throughout the genome. QTL regions contained several genes with known or predicted immune functions, some differentially expressed. The putative functional genes and variants identified could help improve marker-based selection for pancreas disease resistance.

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.

Modeling Pathogen Dispersal in Marine Fish and Shellfish

In marine ecosystems, oceanographic processes often govern host contacts with infectious agents. Consequently, many approaches developed to quantify pathogen dispersal in terrestrial ecosystems have limited use in the marine context. Recent applications in marine disease modeling demonstrate that physical oceanographic models coupled with biological models of infectious agents can characterize dispersal networks of pathogens in marine ecosystems. Biophysical modeling has been used over the past two decades to model larval dispersion but has only recently been utilized in marine epidemiology. In this review, we describe how biophysical models function and how they can be used to measure connectivity of infectious agents between sites, test hypotheses regarding pathogen dispersal, and quantify patterns of pathogen spread, focusing on fish and shellfish pathogens.

Response of the Salmon Heart Transcriptome to Pancreas Disease: Differences Between High- and Low-Ranking Families for Resistance

Pancreas disease caused by salmonid alphaviruses leads to severe losses in Atlantic salmon aquaculture. The aim of our study was to gain a better understanding of the biological differences between salmon with high and low genomic breeding values (H-gEBV and L-gEBV respectively) for pancreas disease resistance. Fish from H- and L-gEBV families were challenged by intraperitoneal injection of salmonid alphavirus or co-habitation with infected fish. Mortality was higher with co-habitation than injection, and for L- than H-gEBV. Heart for RNA-seq and histopathology was collected before challenge and at four- and ten-weeks post-challenge. Heart damage was less severe in injection-challenged H- than L-gEBV fish at week 4. Viral load was lower in H- than L-gEBV salmon after co-habitant challenge. Gene expression differences between H- and L-gEBV manifested before challenge, peaked at week 4, and moderated by week 10. At week 4, H-gEBV salmon showed lower expression of innate antiviral defence genes, stimulation of B- and T-cell immune function, and weaker stress responses. Retarded resolution of the disease explains the higher expression of immune genes in L-gEBV at week 10. Results suggest earlier mobilization of acquired immunity better protects H-gEBV salmon by accelerating clearance of the virus and resolution of the disease.

Infectious Salmon Anemia and Farm-Level Culling Strategies

Infectious salmon anemia (ISA) is an infectious disease, and outbreaks must be handled to avoid spread between salmon sea farms. Intensive culling at infected farms is an important biosecurity measure to avoid further spread but is also a costly intervention that farmers try to avoid. A lack of action, however, may lead to new outbreaks in nearby salmon sea farms, with severe impacts on both economy and animal welfare. Here, we aim to explore how a time delay between a detected outbreak and the culling of both infected cages and entire farms affects the further spread of the disease. We use a previously published model to calculate how many salmon sea farms were directly infected in each outbreak. To investigate the effect of culling on the further spread of disease, we use the number of months elapsed from the detected outbreak to (a) the first cage being depopulated, and (b) to the entire salmon sea farm being depopulated as predictors of how many new farms the virus was transmitted to, after controlling for contact between the farms. We show that the lapse in time before the first cage is depopulated correlates positively with how many new salmon sea farms are infected, indicating that infected cages should be culled with as little time delay as possible. The model does not have sufficient power to separate between culling of only cages assumed to be infected and the entire farm, and, consequently, provides no direct empirical evidence for the latter. Lack of evidence is not evidence, however, and we argue that a high probability of spread between cages in infected salmon sea farms still supports the depopulation of entire farms as the safest option.

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.

Risk Factors Associated With Outbreaks of Infectious Salmon Anemia (ISA) With Unknown Source of Infection in Norway

The occurrence of infectious salmon anemia (ISA) outbreaks in marine farmed Atlantic salmon constitutes a recurring challenge in Norway. Here, we aim to identify risk factors associated with ISA outbreaks with an unknown source of infection (referred to as primary ISA outbreaks). Primary ISA outbreaks are here defined by an earlier published transmission model. We explored a wide range of possible risk factors with logistic regression analysis, trying to explain occurrence of primary ISA with available data from all Norwegian farm sites from 2004 to June 2017. Explanatory variables included site latitude and a range of production and disease data. The mean annual risk of having a primary outbreak of ISA in Norway was 0.7% during this study period. We identified the occurrence of infectious pancreatic necrosis (IPN), having a stocking period longer than 2 months, having the site located at high latitude and high fish density (biomass per cage volume) in the first six months after transfer to sea site as significant risk factors (p < 0.05). We have identified factors related to management routines, other disease problems, and latitude that may help to understand the hitherto unidentified drivers behind the emergence of primary ISA outbreaks. Based on our findings, we also provide management advice that may reduce the incidence of primary ISA outbreaks.

Molecular tracing confirms that infection with infectious pancreatic necrosis virus follows the smolt from hatchery to grow-out farm

Infectious pancreatic necrosis (IPN) is an important restraint to production of salmonids in aquaculture globally. In order to implement efficacious mitigation strategies for control of this disease, it is important to understand infection routes under current production systems. IPN virus has been shown to be transmitted vertically in Rainbow trout, from broodstock to fingerlings in hatcheries, and there is circumstantial evidence suggesting that vertical transmission can also occur in Atlantic salmon, in addition to horizontal transmission between grow-out fish in farms. In this study, we show that the smolt carries infection with IPN from hatchery to the marine farm. We do this by comparing sequences from fish groups taken both in hatcheries and on corresponding marine grow-out farms. We use statistical analysis to prove that sequences obtained from the same fish group in both hatchery and marine farm are more similar than sequences obtained from random fish groups on hatcheries and marine farms.

Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity of this score, together with farm indegree (dichotomized as ≤ 1 or > 1), were assessed through generalized Poisson regression models, in which the modeled outcome was pathogen richness, defined here as the number of different diseases affecting a farm during a year. Seawater salmon (SW salmon) farms had the highest biosecurity scores with a median (interquartile range) of 82.3 (5.4), followed by freshwater salmon (FW salmon) with 75.2 (8.2), and freshwater trout (FW trout) farms with 74.8 (4.5). For FW salmon and trout farms, the top ranked model (in terms of leave-one-out information criteria, looic) was the null model (looic = 46.1). For SW salmon farms, the best ranking model was the full model with both predictors and their interaction (looic = 33.3). Farms with a higher biosecurity score were associated with lower pathogen richness, and farms with indegree > 1 (i.e. more than one fish supplier) were associated with increased pathogen richness. The effect of the interaction between these variables was also important, showing an antagonistic effect. This would indicate that biosecurity effectiveness is achieved through a broader perspective on the subject, which includes a minimization in the number of suppliers and hence in the possibilities for infection to enter a farm. The work presented here could be used to elaborate indicators of a farm’s disease risk based on its biosecurity score and indegree, to inform risk-based disease surveillance and control strategies for private and public stakeholders.

Triploid atlantic salmon (Salmo salar L.) post-smolts accumulate prevalence more slowly than diploid salmon following bath challenge with salmonid alphavirus subtype 3

Triploid Atlantic salmon (Salmo salar L.) may play an important role in the sustainable expansion of the Norwegian aquaculture industry. Therefore, the susceptibility of triploid salmon to common infections such as salmonid alphavirus (SAV), the causative agent of pancreas disease (PD), requires investigation. In this study, shortly after seawater transfer, diploid and triploid post-smolts were exposed to SAV type 3 (SAV3) using a bath challenge model where the infectious dose was 48 TCID50 ml-1 of tank water. Copy number analysis of SAV3 RNA in heart tissue showed that there was no difference in viral loads between the diploids and triploids. Prevalence reached 100% by the end of the 35-day experimental period in both infected groups. However, prevalence accumulated more slowly in the triploid group reaching 19% and 56% at 14 and 21 days post exposure (dpe) respectively. Whereas prevalence in the diploid group was 82% and 100% at the same time points indicating some differences between diploid and triploid fish. Both heart and pancreas from infected groups at 14 dpe showed typical histopathological changes associated with pancreas disease. Observation of this slower accumulation of prevalence following a natural infection route was possible due to the early sampling points and the exposure to a relatively low dose of virus. The triploid salmon in this study were not more susceptible to SAV3 than diploid salmon indicating that they could be used commercially to reduce the environmental impact of escaped farmed fish interbreeding with wild salmon. This is important information regarding the future use of triploid fish in large scale aquaculture where SAV3 is a financial threat to increased production.

The epidemiology of pancreas disease in salmonid aquaculture: a summary of the current state of knowledge

Pancreas disease (PD) is a viral disease caused by Salmonid alphavirus (SAV) that affects farmed Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss (Walbaum)) in the seawater phase. Since its first description in Scotland in 1976, a large number of studies have been conducted relating to the disease itself and to factors contributing to agent spread and disease occurrence. This paper summarizes the currently available, scientific information on the epidemiology of PD and its associated mitigation and control measures. Available literature shows infected farmed salmonids to be the main reservoir of SAV. Transmission between seawater sites occurs mainly passively by water currents or actively through human activity coupled with inadequate biosecurity measures. All available information suggests that the current fallowing procedures are adequate to prevent agent survival within the environment through the fallowing period and thus that a repeated disease outbreak at the same site is due to a new agent introduction. There has been no scientific evaluation of currently used on-site biosecurity measures, and there is limited information on the impact of available mitigation measures and control strategies.

Technical pre-analytical effects on the clinical biochemistry of Atlantic salmon (Salmo salar L.)

Clinical biochemistry has long been utilized in human and veterinary medicine as a vital diagnostic tool, but despite occasional studies showing its usefulness in monitoring health status in Atlantic salmon (Salmo salar L.), it has not yet been widely utilized within the aquaculture industry. This is due, in part, to a lack of an agreed protocol for collection and processing of blood prior to analysis. Moreover, while the analytical phase of clinical biochemistry is well controlled, there is a growing understanding that technical pre-analytical variables can influence analyte concentrations or activities. In addition, post-analytical interpretation of treatment effects is variable in the literature, thus making the true effect of sample treatment hard to evaluate. Therefore, a number of pre-analytical treatments have been investigated to examine their effect on analyte concentrations and activities. In addition, reference ranges for salmon plasma biochemical analytes have been established to inform veterinary practitioners and the aquaculture industry of the importance of clinical biochemistry in health and disease monitoring. Furthermore, a standardized protocol for blood collection has been proposed.

Relationship between viral dose and outcome of infection in Atlantic salmon, Salmo salar L., post-smolts bath-challenged with salmonid alphavirus subtype 3

Salmonid alphavirus subtype 3 (SAV3) causes pancreas disease (PD) and adversely affects salmonid aquaculture in Europe. A better understanding of disease transmission is currently needed in order to manage PD outbreaks. Here, we demonstrate the relationship between viral dose and the outcome of SAV3 infection in Atlantic salmon post-smolts using a bath challenge model. Fish were challenged at 12 °C with 3 different SAV3 doses; 139, 27 and 7 TCID₅₀ L⁻¹ of seawater. A dose of as little as 7 TCID₅₀ L⁻¹ of seawater was able to induce SAV3 infection in the challenged population with a substantial level of variation between replicate tanks and, therefore, likely represents a dose close to the minimum dose required to establish an infection in a population. These data also confirm the highly infectious nature of SAV through horizontal transmission. The outcome of SAV3 infection, evaluated by the prevalence of viraemic fish, SAV3-positive hearts, and the virus shedding rate, was positively correlated to the original SAV3 dose. A maximal shedding rate of 2.4 × 10⁴ TCID₅₀ L⁻¹ of seawater h⁻¹ kg⁻¹ was recorded 10 days post-exposure (dpe) from the highest dose group. The method reported here, for the quantification of infectious SAV3 in seawater, could be useful to monitor PD status or obtain data from SAV3 outbreaks at field locations. This information could be incorporated into pathogen dispersal models to improve risk assessment and to better understand how SAV3 spreads between farms during outbreaks. This information may also provide new insights into the control and mitigation of PD.

Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy

Infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) are the most important viral pathogens impacting rainbow trout farming. These viruses are persistent in Italy, where they are responsible for severe disease outbreaks (epizootics) that affect the profitability of the trout industry. Despite the importance of IHNV and VHSV, little is known about their evolution at a local scale, although this is likely to be important for virus eradication and control. To address this issue we performed a detailed molecular evolutionary and epidemiological analysis of IHNV and VHSV in trout farms from northern Italy. Full-length glycoprotein gene sequences of a selection of VHSV (n = 108) and IHNV (n = 89) strains were obtained. This revealed that Italian VHSV strains belong to sublineages Ia1 and Ia2 of genotype Ia and are distributed into 7 genetic clusters. In contrast, all Italian IHNV isolates fell within genogroup E, for which only a single genetic cluster was identified. More striking was that IHNV has evolved more rapidly than VHSV (mean rates of 11 and 7.3 × 10⁻⁴ nucleotide substitutions per site, per year, respectively), indicating that these viruses exhibit fundamentally different evolutionary dynamics. The time to the most recent common ancestor of both IHNV and VHSV was consistent with the first reports of these pathogens in Italy. By combining sequence data with epidemiological information it was possible to identify different patterns of virus spread among trout farms, in which adjacent facilities can be infected by either genetically similar or different viruses, and farms located in different water catchments can be infected by identical strains. Overall, these findings highlight the importance of combining molecular and epidemiological information to identify the determinants of IHN and VHS spread, and to provide data that is central to future surveillance strategies and possibly control.

Vaccination against pancreas disease in Atlantic salmon, Salmo salar L., reduces shedding of salmonid alphavirus

Salmon pancreas disease virus, often referred to as salmonid alphavirus (SAV), causes pancreas disease (PD) in European salmonids. SAV transmits horizontally from fish shedding virus into the water and ocean currents are believed to be a main contributor of viral spread between marine farms. Vaccination against PD is previously shown to reduce mortality and severity of clinical PD. In this study, we demonstrate that vaccination against PD significantly reduces viral shedding from infected individuals. The results suggest that PD vaccination can be an important tool to reduce the infection pressure, a known key risk for PD outbreaks at neighbouring farms.

Liquid fat, a potential abiotic vector for horizontal transmission of salmonid alphavirus?

Viral diseases represent serious challenge in marine farming of Atlantic salmon (Salmo salar L). Pancreas disease (PD) caused by a salmonid alphavirus (SAV) is by far the most serious in northern Europe. To control PD, it is necessary to identify virus transmission routes. One aspect to consider is whether the virus is transported as free particles or associated with potential vectors. Farmed salmonids have high lipid content in their tissue which may be released into the environment from decomposing dead fish. At the seawater surface, the effects of wind and ocean currents are most prominent. The aim of this study was primarily to identify whether the lipid fraction leaking from dead infected salmon contains SAV. Adipose tissue from dead SAV-infected fish from three farming sites was submerged in beakers with sea water in the laboratory and stored at different temperature and time conditions. SAV was identified by real-time RT-PCR in the lipid fractions accumulating at the water surface in the beakers. SAV-RNA was also present in the sea water. Lipid fractions were transferred to cell culture, and viable SAV was identified. Due to its hydrophobic nature, fat with infective pathogenic virus at the surface may contribute to long-distance transmission of SAV.

Genetic characterization of salmonid alphavirus in Norway

Pancreas disease (PD), caused by salmonid alphavirus subtype 3 (SAV3), emerged in Norwegian aquaculture in the 1980s and is now endemic along the south-western coast. In 2011, the first cases of PD caused by marine salmonid alphavirus subtype 2 (SAV2) were reported. This subtype has spread rapidly among the fish farms outside the PD-endemic zone and is responsible for disease outbreaks at an increasing numbers of sites. To describe the geographical distribution of salmonid alphavirus (SAV), and to assess the time and site of introduction of marine SAV2 to Norway, an extensive genetic characterization including more than 200 SAV-positive samples from 157 Norwegian marine production sites collected from May 2007 to December 2012 was executed. The first samples positive for marine SAV2 originated from Romsdal, in June 2010. Sequence analysis of the E2 gene revealed that all marine SAV2 included in this study were nearly identical, suggesting a single introduction into Norwegian aquaculture. Further, this study provides evidence of a separate geographical distribution of two subtypes in Norway. SAV3 is present in south-western Norway, and marine SAV2 circulates in north-western and Mid-Norway, a geographical area which since 2010 constitutes the endemic zone for marine SAV2.

Routine clinical inspections in Norwegian marine salmonid sites: A key role in surveillance for freedom from pathogenic viral haemorrhagic septicaemia (VHS)

Since the mid-1980s, clinical inspections of aquaculture sites carried out on a regular basis by authorized veterinarians and fish health biologists (known as fish health services: FHS) have been an essential part of aquatic animal health surveillance in Norway. The aims of the present study were (1) to evaluate the performance of FHS routine clinical inspections for the detection of VHS and (2) to explore the effectiveness of risk-based prioritisation of FHS inspections for demonstrating freedom from VHS in marine salmonid sites in Norway. A stochastic simulation model was developed to estimate site sensitivity (SeS), population sensitivity (SeP), and probability of freedom (PFree). The estimation of SeS takes into consideration the probability that FHS submit samples if a site is infected, the probability that a sample is tested if submitted, the effective probability of infection in fish with clinical signs, laboratory test sensitivity, and the number of tested samples. SeP and PFree were estimated on a monthly basis over a 12 month period for six alternative surveillance scenarios and included the risk factors: region, species, area production density, and biosecurity level. Model results indicate that the current surveillance system, based on routine inspections by the FHS has a high capability for detecting VHS and that there is a high probability of freedom from VHS in Norwegian marine farmed salmonids (PFree >95%). Sensitivity analysis identified the probabilities that samples are submitted and submitted samples are tested, as the most influential input variables. The model provides a supporting tool for evaluation of potential changes in the surveillance strategy, and can be viewed as a platform for similar exotic viral infectious diseases in marine salmonid farming in Norway, if they share similar risk factors.

Space-time modelling of the spread of pancreas disease (PD) within and between Norwegian marine salmonid farms

Infectious diseases are a constant threat to industrialised farming, which is characterised by high densities of farms and farm animals. Several mathematical and statistical models on spatio-temporal dynamics of infectious diseases in various farmed host populations have been developed during the last decades. Here we present a spatio-temporal stochastic model for the spread of a disease between and within aquaculture farms. The spread between farms is divided into several transmission pathways, including (i) distance related spread and (ii) other types of contagious contacts. The within-farm infection dynamics is modelled by a susceptible-infected-recovered (SIR) model. We apply this framework to model the spread of pancreas disease (PD) in salmon farming, using data covering all farms producing salmonids over 9 years in Norway. The motivation for the study was partly to unravel the spatio-temporal dynamics of PD in salmon farming and partly to use the model for scenario simulation of PD control strategies. We find, for example, that within-farm infection dynamics vary with season and we provide estimates of the timing from unobserved infection events to disease outbreaks on farms are detected. The simulations suggest that if a strategy involving culling of infectious cohorts is implemented, the number of detected disease outbreaks per year may be reduced by 57% after the full effect has been reached. We argue that the high detail and coverage of data on salmonid production and disease occurrence should encourage the use of simulation modelling as a means of testing effects of extensive control measures before they are implemented in the salmon farming industry.

Risk factors for outbreaks of infectious pancreatic necrosis (IPN) and associated mortality in Norwegian salmonid farming

Infectious pancreatic necrosis (IPN) has for many years been considered one of the most important restraints to the production of salmonids in European aquaculture. In Norway, the disease is responsible for high losses in post-smolts in the first few weeks after sea transfer. Despite the importance of IPN, there are few epidemiological studies on risk factors and mitigation strategies. In this paper, we present analyses of data from all cohorts put to sea in 2009 to 2012 on Norwegian marine salmonid farms. The data used were obtained from national registers on salmonid production and disease outbreaks. The results showed that the risk of IPN outbreak was higher for spring versus autumn cohorts, Atlantic salmon versus rainbow trout and for cohorts on farms with previous history of IPN. The risk increased with increasing cohort size and infection pressure, whereas increasing temperature and weight at sea transfer decreased the risk. Estimations from a model of cumulative mortality within the first 6 mo after sea transfer showed that mortality in cohorts with IPN increased to approximately 7.2% as compared to a 'baseline' cohort with a mortality of 3.4%. If the cohort had both IPN and pancreas disease (PD), the estimated mortality increased to 12.9%, and cohorts with both IPN, PD and heart and skeletal muscle inflammation (HSMI) had an estimated mortality of 16.6%, when all other significant factors were kept constant (these were cohort type, year, temperature at sea transfer and weight at sea transfer). Our results provide valuable inputs for mitigation strategies and for economic modelling of consequences of disease.

Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h²~0.5; post-smolt POP 2 h²~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.

Clinical manifestations of pancreas disease outbreaks in Norwegian marine salmon farming - variations due to salmonid alphavirus subtype

Pancreas disease (PD) in Norwegian salmonid aquaculture has traditionally been caused by salmonid alphavirus (SAV) subtype 3. Following the isolation of a novel SAV subtype in 2010, marine SAV2, two separate endemic areas have developed. It has been debated whether disease outbreaks due to marine SAV2 result in milder clinical manifestations compared to outbreaks caused by SAV3. The aim of this study was to descriptively investigate site-level differences in the clinical manifestations of marine SAV2 and SAV3 at Norwegian seawater sites diagnosed with PD in 2012. The findings suggest that Norwegian PD outbreaks caused by marine SAV2 result in lower mortality and milder clinical signs compared to outbreaks caused by SAV3. For sites without reported PD-related mortality, there was no difference in the mortality levels between sites infected by marine SAV2 and SAV3. The results also indicate that there are no differences in grading quality at slaughter between the SAV subtypes.

An experimental means of transmitting pancreas disease in Atlantic salmon Salmo salar L. fry in freshwater

A challenge model for pancreas disease in Atlantic salmon, Salmo salar L. fry, was developed comparing two salmonid alphavirus (SAV) subtypes: SAV1 and SAV5. Viral doses of 3 × 10(5) TCID50  mL(-1) for SAV1 and 3 × 10(4) for SAV5 were tested in triplicate tanks, each containing 450 salmon fry. Cumulative mortalities of 1.2% were recorded. Titres of virus recovered from the mortalities ranged from 10(2) to 10(7) TCID50  mL(-1) . Fry were sampled at 3, 5 and 7.5 weeks post-challenge. Sampling after 3 weeks revealed a high prevalence of infection in the absence of clinical signs, and infectious virus was recovered from 80% and 43% of sampled fry infected with SAV1 and SAV5, respectively. After 5 weeks pancreas, heart and red skeletal muscle lesions were generally observed, whilst degeneration in white skeletal muscle was observed only in fish infected with SAV1. In situ hybridisation confirmed the presence of viral genome in infected pancreas, heart and muscle. After 7.5 weeks, infectious virus (both isolates) was recovered from 13.3% of the fish sampled, with a viral titre of 10(2) TCID50  mL(-1) . Clearly, salmon fry are susceptible to SAV infection and pancreas disease.

Large scale modelling of salmon lice (Lepeophtheirus salmonis) infection pressure based on lice monitoring data from Norwegian salmonid farms

Infection by parasitic sea lice is a substantial problem in industrial scale salmon farming. To control the problem, Norwegian salmonid farms are not permitted to exceed a threshold level of infection on their fish, and farms are required to monitor and report lice levels on a weekly basis to ensure compliance with the regulation. In the present study, we combine the monitoring data with a deterministic model for salmon lice population dynamics to estimate farm production of infectious lice stages. Furthermore, we use an empirical estimate of the relative risk of salmon lice transmission between farms, that depend on inter-farm distances, to estimate the external infection pressure at a farm site, i.e. the infection pressure from infective salmon lice of neighbouring farm origin. Finally, we test whether our estimates of infection pressure from neighbouring farms as well as internal within farm infection pressure, predicts subsequent development of infection in cohorts of farmed salmonids in their initial phase of marine production. We find that estimated external infection pressure is a main predictor of salmon lice population dynamics in newly stocked cohorts of salmonids. Our results emphasize the importance of keeping the production of infectious lice stages at low levels within local networks of salmon farms. Our model can easily be implemented for real time estimation of infection pressure at the national scale, utilizing the masses of data generated through the compulsory lice monitoring in salmon farms. The implementation of such a system should give the salmon industry greater predictability with respect to salmon lice infection levels, and aid the decision making process when the development of new farm sites are planned.

Seasonal increase in sea temperature triggers pancreas disease outbreaks in Norwegian salmon farms

Pancreas disease (PD) is a viral disease causing negative impacts on economy of salmon farms and fish welfare. Its transmission route is horizontal, and water transport by ocean currents is an important factor for transmission. In this study, the effect of temperature changes on PD dynamics in the field has been analysed for the first time. To identify the potential time of exposure to the virus causing PD, a hydrodynamic current model was used. A cohort of salmon was assumed to be infected the month it was exposed to virus from other infective cohorts by estimated water contact. The number of months from exposure to outbreak defined the incubation period, which was used in this investigation to explore the relationship between temperature changes and PD dynamics. The time of outbreak was identified by peak in mortality based on monthly records from active sites. Survival analysis demonstrated that cohorts exposed to virus at decreasing sea temperature had a significantly longer incubation period than cohorts infected when the sea temperature was increasing. Hydrodynamic models can provide information on the risk of being exposed to pathogens from neighbouring farms. With the knowledge of temperature-dependent outbreak probability, the farmers can emphasize prophylactic management, avoid stressful operations until the sea temperature is decreasing and consider removal of cohorts at risk, if possible.

The effect of allostatic load on hypothalamic-pituitary-interrenal (HPI) axis before and after secondary vaccination in Atlantic salmon postsmolts (Salmo salar L.)

The experiment consisted of three experimental groups: (1) "vaccine and stress", (2) "stress and vaccine" and (3) control. All groups have previously been vaccinated 6 months prior to the start of the experiment. At the start of the experiment, the "vaccine and stress" group was vaccinated with Pentium Forte Plus for the second time (25.02.2008) and then given a daily stressor (confinement stressor 267 kg m-3 in 15 min) for a period of 4 weeks. The "stress and vaccine" group was given a similar daily stressor for 4 weeks and then vaccinated for the second time. The control group was neither stressed nor vaccinated a second time. The results indicates that fish in the "stress and vaccine" group may have entered an allostatic overload type 2 due to oversensitivity to ACTH, a reduced efficient negative feedback system with elevated baseline levels of plasma cortisol and reduced immune response with pronounced effects on the well-being of the animal. The "vaccine and stress" group may likewise have entered an allostatic overload type 1 response, with oversensitivity to ACTH and transient reduced efficient negative feedback system. This study shows that if plasma cortisol becomes elevated prior to vaccination, it could perhaps instigate an allostatic overload type 2 with dire consequences on animal welfare. To reduce the risk of compromising the animal welfare during commercial vaccination of salmon, one propose to grade the fish minimum a week prior to vaccination or grade simultaneously with vaccination. This could reduce the overall allostatic load during handling and vaccination and secure a healthy fish with intact immune response and improved animal welfare.

Spatial and temporal dynamics of mass mortalities in oysters is influenced by energetic reserves and food quality

Although spatial studies of diseases on land have a long history, far fewer have been made on aquatic diseases. Here, we present the first large-scale, high-resolution spatial and temporal representation of a mass mortality phenomenon cause by the Ostreid herpesvirus (OsHV-1) that has affected oysters (Crassostrea gigas) every year since 2008, in relation to their energetic reserves and the quality of their food. Disease mortality was investigated in healthy oysters deployed at 106 locations in the Thau Mediterranean lagoon before the start of the epizootic in spring 2011. We found that disease mortality of oysters showed strong spatial dependence clearly reflecting the epizootic process of local transmission. Disease initiated inside oyster farms spread rapidly beyond these areas. Local differences in energetic condition of oysters, partly driven by variation in food quality, played a significant role in the spatial and temporal dynamics of disease mortality. In particular, the relative contribution of diatoms to the diet of oysters was positively correlated with their energetic reserves, which in turn decreased the risk of disease mortality.

Transmission dynamics of pancreas disease (PD) in a Norwegian fjord: aspects of water transport, contact networks and infection pressure among salmon farms

Pancreas disease (PD) in marine salmon farming is caused by salmon pancreas disease virus (SPDV). Virus survival, infection pressure and contact networks among farms influence the potential of PD to spread. The present study aims to explore contact networks and infection pressure and their ability to explain transmission dynamics of PD in a Norwegian fjord. In this study, we included all records of PD by subtype 3 (SPDV3) in the study population from the first reported in August 2006 to the last reported in November 2009. Using logistic regression analyses, we found that contact network by water transport explained better transmission of PD than contact networks defined by ownership or close distance to infected farms. Hydrodynamic modelling can be a valuable tool to forecast the spread of PD and thereby take actions to reduce the transmission. Knowing the risk of getting infected, it is important to avoid water transport from infected farms when new cohorts are transferred to sea water, and to have conscious control regarding management operations between farms.

Risk factors for cardiomyopathy syndrome (CMS) in Norwegian salmon farming

Cardiomyopathy syndrome (CMS) has been an economically important disease in Norwegian aquaculture since the 1990s. In this study, data on monthly production characteristics and case registrations were combined in a cohort study and supplemented with a questionnaire-based case-control survey on management factors in order to identify risk factors for CMS. The cohort study included cases and controls from 2005 to 2012. From this dataset differences between all cases and controls were analyzed by a mixed effect multivariate logistic regression. From this we found that the probability of CMS increased with increasing time in the sea, infection pressure, and cohort size, and that cohorts which had previously been diagnosed with heart and skeletal muscle inflammation or which were in farms with a history of CMS in previous cohorts had double the odds of developing CMS. The model was then used to calculate the predicted value for each cohort from which additional data were obtained via the questionnaire-based survey and used as offset for calculating the probability of CMS in a semi-univariate analysis of additional risk factors. Finally, the model was used to calculate the probability of developing CMS in 100 different scenarios in which the cohorts were subject to increasingly worse conditions with regards to the risk factors from the dataset. We believe that this exercise is a good way of communicating the findings to farmers, so they can make informed decisions when trying to avoid CMS in their fish cohorts.

Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture

Salmonid alphavirus (SAV) causes infections in farmed Atlantic salmon and rainbow trout in Europe. Genetic diversity exists among SAV strains from farmed fish and six subtypes have been proposed based on genetic distance. Here, we used six full-genome sequences and 71 partial sequences of the structural ORF to estimate the evolutionary rate of SAV. The rate, 2.13×10(-4) nt substitutions per site per year, was further used to date evolutionary events in a Bayesian phylogenetic framework. The comparison of these dates with known historical events suggested that all six subtypes diverged prior to the twentieth century, earlier than the first attempts to introduce and farm rainbow trout in Europe. The subtypes must therefore have existed in a wild reservoir, as yet unidentified. The strains of each subtype, with the exception of subtype 2, have a common ancestor that existed after the 1970s - the start of modern farming of Atlantic salmon. These ancestors are likely to represent the independent introductions to farmed fish populations from the wild reservoir. The subtypes have developed subsequently into self-sustainable epizootics. The most parsimonious phylogeographic reconstruction suggested that the location of the wild reservoir is in or around the North Sea. After the initial introductions to aquaculture, further transmission of SAV was likely related to the industry infrastructure. This was exemplified by the finding of genetically identical subtype 2 and 3 strains separated by large geographical distances, as well as genetically distinct co-circulating lineages within the same geographical area.

Spatial distribution of mortality in Pacific oysters Crassostrea gigas: reflection on mechanisms of OsHV-1 transmission

The ostreid herpesvirus OsHV-1 has the potential to devastate Pacific oyster Crassostrea gigas culture in Australia as it has done in many other countries, highlighting the need for a better understanding of disease expression and transmission. The aim of this study was to assess the spatial distribution of OsHV-1-associated mortalities in one of only two infected areas in Australia, Woolooware Bay (Botany Bay, New South Wales). In October 2011, healthy sentinel Pacific oysters were placed in 3 different locations at 3 different tidal levels, and OsHV-1 associated mortalities were closely monitored over 7 mo. The outbreak started in November 2011, and the disease remained active until April 2012. Three major mortality events were detected. Rather than being a propagating epizootic, it appeared that most oysters were infected from a common environmental source. The distribution of OsHV-1-associated mortalities was spatially clustered, highly variable and clearly dependent on the age of oysters and their position in the water column. Non-random distribution of mortalities at macro scale (sites several km apart) and micro scale (within rearing trays), and vertical clustering patterns in the water column are discussed in regard to factors known to influence mechanism of disease transmission in aquatic environments (hydrodynamics, physical disturbances, host density/distribution, and variations of environmental parameters). A new hypothesis proposing that OsHV-1 may be carried through water by particles, possibly plankton, is also suggested to explain the patchy distribution of mortalities in Woolooware Bay.

Mortality related to pancreas disease in Norwegian farmed salmonid fish, Salmo salar L. and Oncorhynchus mykiss (Walbaum)

High mortality during the salmonid seawater phase is a continuous problem for the salmonid aquaculture industry, although the mortality levels show a large variation both in farms with a disease history and those without. We wanted to examine the mortality patterns in farms with pancreas disease (PD) and compare it to farms without this diagnosis. Further, we wished to investigate the factors influencing the maximum mortality in both groups. We examined data from all salmonid farms in Norway stocked after January 2003 and slaughtered before December 2007. In total, 1884 cohorts were included, and 150 of these were diagnosed with PD. We found that season accounted for more of the variation in mortality than water temperature in PD-positive cohorts and that infection pressure influenced the mortality in non-PD cohorts, suggesting outbreaks of disease that are not diagnosed. We also found that the mortality in PD cohorts decreased significantly from 2003 to 2007, suggesting that increased knowledge about PD and targeted actions have been effective. Our study further suggests that crude mortality figures may be of limited use when wanting to examine a particular disease and risk factors for increased mortality. We suggest farmers and legislation should turn to a more modern approach with cause-specific mortality records.

Immune parameters correlating with reduced susceptibility to pancreas disease in experimentally challenged Atlantic salmon (Salmo salar)

Two strains of Atlantic salmon (Salmon salar) with different susceptibility to infectious salmon anaemia (ISA) were challenged with salmon pancreas disease virus (SPDV), the etiological agent of salmon pancreas disease (PD), by cohabitation. Serum and tissues were sampled at 0, 1, 3, 6 and 8 weeks post-challenge. Experimental challenge with SAV did not cause mortality, but virus loads and assessment of histopathology indicated that the fish more resistant to ISAV (ISAHi) also was more resistant to PD. Eight weeks post-challenge, the ISAHi strain had higher titres of SAV-neutralising antibodies than the less resistant strain (ISALo). Transcript levels of four adaptive and six innate immune parameters were analysed by real-time RT-PCR in heart, head kidney (HK) and gills of both strains. Secretory IgM (sIgM) and CD8 levels differed most between the two salmon strains. The ISAHi strain had significantly higher levels of sIgM in HK at all samplings, and significantly higher CD8 levels in gills at most samplings. In heart, both sIgM and CD8 levels increased significantly during the challenge, but the increase appeared earlier for the ISALo strain. By hierarchical clustering analysis of mRNA levels, a clear segregation was observed between the two strains prior to the virus challenge. As the viral infection developed, the clustering divide between fish strains disappeared, first for innate and later for adaptive parameters. At eight weeks post-challenge, the divide had however reformed for adaptive parameters. Possible pair-wise correlation between transcript levels of immune parameters was evaluated by a non-parametric statistical test. For innate parameters, the extent of correlation peaked at 3 wpc in all tissues; this came rapidly for ISALo and more gradual for ISAHi. The ISAHi strain tended to show higher correlation for innate parameters in heart and gill than ISALo at early sampling times. For adaptive immune parameters, little correlation was observed in general, except for ISAHi in heart at 6 wpc. Overall, the observed differences in immune parameters may provide important clues to the causes underlying the observed difference in susceptibility to PD.

A comparison of modelling approaches to assess the transmission of pathogens between Scottish fish farms: the role of hydrodynamics and site biomass

Scotland is the largest Atlantic salmon (Salmo salar) producer in the EU with an output of over 150,000 t, contributing over £500 million annually towards the economy. Production continues to increase, predominantly due to the increase in output per farm and reduction in losses due to infectious diseases. Farms are grouped within disease management areas whose boundaries are defined by where the closest pair of farms is separated by more than twice the tidal excursion distance (TE) Tidal excursion is defined as 7.2 km in mainland Scotland, or 3.6 km in the Shetland Islands). The majority of salmon farms are located within relatively sheltered inshore areas where non-tidal advective current speed is minimal. However there is an aspiration for offshore production where it might be possible to increase stocking levels and where current speeds will be greater so TE models could break down. Separation distances whereby farms would avoid infection risk were obtained using an analytical, discrete-time Susceptible-Exposed-Infectious-Recovered (SEIR) model coupled with a hydrodynamic transport expression representing transmission of pathogenic agents between fish farms. The model incorporated transmission, expression and recovery parameters as well as pathogen shedding and decay. The simplified hydrodynamic model incorporated residual advection, tidal advection and turbulent diffusion elements. The obtained separation distances were compared to a computationally intensive, numerical model and were demonstrated to be comparable, although the analytical model underestimated the variation within the transmission distances. Applying characteristics for a robust pathogen, infectious pancreatic necrosis virus type (IPNV-type), and less robust pathogens such as infectious salmon anaemia virus type (ISAV-type) and Aeromonas salmonicida type (AS-type) pathogens, it was possible to obtain separation distances whereby farms avoided infection. Simulation outputs indicated that separation distances should increase to avoid disease as farm size and current speed increase. The more conserved IPNV-type pathogen required separation distances of hundreds of kilometres, AS-type required tens of kilometres, whilst the distances for ISAV-type were within the scale of the current DMAs, that were developed for ISAV control. However, should production be moved to areas of faster moving currents and increased farm production the current disease management area principles might need readdressing.

Cohort study of effect of vaccination on pancreas disease in Norwegian salmon aquaculture

Pancreas disease (PD) is an economically important viral disease in Norwegian aquaculture, with 75 to 89 annual outbreaks from 2009 to 2011. To hinder further spread of disease from an initial endemic area on the west coast of Norway, measures for surveillance and control are in place, and the disease is notifiable on a national level. Since 2008, the Norwegian coastline has been divided into 2 administrative zones separated by a production-free area of 10 nautical miles at approximately 63°N. At the same time, a vaccination program involving most marine salmonid farms was initiated by the industry, using a vaccine against PD that was made commercially available in 2007. The effects of the vaccine in the field have been questioned, since the annual number of PD outbreaks has not decreased as expected. However, other production parameters can be used for evaluation of vaccine effect, and in this study the effects of vaccination on cumulative mortality, growth rate, feed conversion factor and number of discarded fish were analyzed using data collected from fish cohorts with and without PD put to sea between spring 2007 and spring 2009. The results show that vaccination against PD has a positive effect in reducing the number of outbreaks, and decreasing cumulative mortality and the number of fish discarded at slaughter.

Low virulent infectious salmon anaemia virus (ISAV-HPR0) is prevalent and geographically structured in Norwegian salmon farming

Infectious salmon anaemia (ISA) is a severe disease in farmed Atlantic salmon Salmo salar that has caused epidemic outbreaks in most salmon-producing countries worldwide. The disease is caused by virulent ISA virus (ISAV). Low virulent variants of the virus, characterised by a full-length sequence in the highly polymorphic region of segment 6 in the virus genome, have been reported with increasing frequencies. These variants of the virus, termed HPR0, have been proposed to be ancestors of virulent ISAV. We examined this idea through studies of the phylogeographic and environmental distribution of ISAV-HPR0, as well as phylogeographic associations between virulent ISAV and ISAV-HPR0. Samples from 232 fish groups were screened for ISAV. Real-time RT-PCR was used for detection of ISAV, and the ISAV haemagglutinin esterase (HE) gene was characterised for positive samples. A Mantel test was used to test phylogeographic associations between pairs of ISAV-HPR0 HE gene sequences. A rank test was used to test associations between HE gene sequences from virulent ISAV and ISAV-HPR0. ISAV-HPR0 was detected in fish groups both in freshwater and marine environments, and in juveniles, on-grown marine salmon and broodstock salmon. Genetic and geographic distances between pairs of ISAV-HPR0 HE gene sequences were positively correlated, suggesting that the population of ISAV-HPR0 is geographically structured. Finally, we found a spatial association between fish groups with virulent ISAV (n = 21) and fish groups with ISAV-HPR0 (n = 27), supporting the hypothesis that ISAV-HPR0 may undergo a transition to virulent ISAV.

Geographical distribution of salmonid alphavirus subtypes in marine farmed Atlantic salmon, Salmo salar L., in Scotland and Ireland

Sequence data from salmonid alphavirus (SAV) strains obtained from farmed marine Atlantic salmon, Salmo salar L. , over a 20-year period between 1991 and 2011 was reviewed to examine the geographical distribution of the genetically defined SAV subtypes in twelve regions across Ireland and Scotland. Of 160 different Atlantic salmon SAV strains examined, 62 belonged to subtype 1, 28 to subtype 2, 34 to subtype 4, 35 to subtype 5 and 1 to subtype 6. SAV subtypes 1, 4 and 6 were found in Ireland, while subtypes 1, 2, 4 and 5 were found in Scotland. In the majority of regions, there was a clear clustering of subtypes, with SAV subtype 1 being the dominant subtype in Ireland overall, as well as in Argyll and Bute in Scotland. SAV subtype 2 predominated in the Shetland and Orkney Islands. The emergence in Atlantic salmon of subtype 2 strains typically associated with sleeping disease in rainbow trout in Argyll and Bute, strongly suggesting transmission of infection between these species, was noted for the first time. SAV subtype 4 was the most common subtype found in the southern Western Isles, while SAV subtype 5 predominated in the northern Western Isles and north-west mainland Scotland. No single strain was dominant on sites in the western Highlands, with a number of sites in this region in particular having more than one subtype detected in different submissions. The significance of these results in relation to aspects of the epidemiology of infection, including transmission, biosecurity and wildlife reservoirs are discussed and knowledge gaps identified.