Triploid Atlantic salmon (Salmo salar) may have increased risk of primary field outbreaks of infectious salmon anaemia.

The impact that escaped farmed fish may have on wild populations is of major concern for Atlantic salmon (Salmo salar) farming. Triploid fish, being infertile, were originally introduced to mitigate the genetic impact of escaped fish. In the recent years, an increase in the number of infectious salmon anaemia (ISA) outbreaks in Norway has been observed, mainly in the northern parts, which is also where farming of triploid fish has been licensed. The present study investigated the susceptibility of triploid Atlantic salmon to ISA both by field observations and experimental infections. Based on field observations, we found an increased susceptibility, with 9.4 increased odds to primary ISA outbreaks in triploid fish versus diploid fish at production-site level, and a tendency of increased odds (3.4) of ISA in triploid fish at individual cage level at sited with primary outbreaks. At some sites, ISA outbreaks were only diagnosed in cages with triploid fish and not in cages with diploid fish. Primary ISA outbreaks are the source for further spread of the disease, and it is noteworthy that in an experimental trial we found significantly more viral RNA in non-ISA-vaccinated triploid than in non-ISA-vaccinated diploid fish at the peak of the infection. Interestingly, the notable differences of susceptibility to ISA for non-ISA vaccinated diploid and triploid fish observed in field were not repeated experimentally. The possible increased risk of ISA should be considered when evaluating the costs and benefits of triploid salmon in farming. It is recommended to keep triploid and diploid fish in biosecure separated sites, or that triploid fish are not farmed at all.

Analysing mortality patterns in salmon farming using daily cage registrations.

This study describes the patterns of mortality and investigates the sources of variation in mortality during the marine phase of commercial salmon farming. The study included daily mortality records from stocking to harvest of 21 million salmon from ten hatcheries in 136 fish-groups (fish in the same cage from the same hatchery). The fish was stocked in 2017-2018 at 21 marine farms within two Norwegian companies. The sources of variation in mortality were investigated using multilevel linear regression models with 'fish-group' nested within 'farm' as a random effect, cross-classified with 'hatchery'. In the final model, 'fish-group' was the source of most variation (70%). Furthermore, the mortality categories 'smolt-related mortality', 'infectious diseases' and 'handling and treatment' were responsible for 10%, 17% and 29% of the total number of dead fish respectively. Overall, the study shows that smolt-related mortality is one of the major causes of death in the first part of the production, while handling and treatment was the dominating cause of mortality in total. Mortality varied by fish-group to a large extent. This means that targeted preventive strategies to decrease mortality for individual fish-groups might be more effective than overall measures at farm or hatchery level.

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.

Genetic background and embryonic temperature affect DNA methylation and expression of myogenin and muscle development in Atlantic salmon (Salmo salar).

The development of ectothermic embryos is strongly affected by incubation temperature, and thermal imprinting of body growth and muscle phenotype has been reported in various teleost fishes. The complex epigenetic regulation of muscle development in vertebrates involves DNA methylation of the myogenin promoter. Body growth is a heritable and highly variable trait among fish populations that allows for local adaptations, but also for selective breeding. Here we studied the epigenetic effects of embryonic temperature and genetic background on body growth, muscle cellularity and myogenin expression in farmed Atlantic salmon (Salmo salar). Eggs from salmon families with either high or low estimated breeding values for body growth, referred to as Fast and Slow genotypes, were incubated at 8°C or 4°C until the embryonic 'eyed-stage' followed by rearing at the production temperature of 8°C. Rearing temperature strongly affected the growth rates, and the 8°C fish were about twice as heavy as the 4°C fish in the order Fast8>Slow8>Fast4>Slow4 prior to seawater transfer. Fast8 was the largest fish also at harvest despite strong growth compensation in the low temperature groups. Larval myogenin expression was approximately 4-6 fold higher in the Fast8 group than in the other groups and was associated with relative low DNA methylation levels, but was positively correlated with the expression levels of the DNA methyltransferase genes dnmt1, dnmt3a and dnmt3b. Juvenile Fast8 fish displayed thicker white muscle fibres than Fast4 fish, while Slow 8 and Slow 4 showed no difference in muscle cellularity. The impact of genetic background on the thermal imprinting of body growth and muscle development in Atlantic salmon suggests that epigenetic variation might play a significant role in the local adaptation to fluctuating temperatures over short evolutionary time.

Associations between piscine reovirus infection and life history traits in wild-caught Atlantic salmon Salmo salar L. in Norway.

Piscine Reovirus (PRV), the putative causative agent of heart and skeletal muscle inflammation (HSMI), is widely distributed in both farmed and wild Atlantic salmon (Salmo salar L.) in Norway. While HSMI is a common and commercially important disease in farmed Atlantic salmon, the presence of PRV has so far not been associated with HSMI related lesions in wild salmon. Factors associated with PRV-infection were investigated in returning Atlantic salmon captured in Norwegian rivers. A multilevel mixed-effect logistic regression model confirmed clustering within rivers and demonstrated that PRV-infection is associated with life-history, sex, catch-year and body length as a proxy for sea-age. Escaped farmed salmon (odds ratio/OR: 7.32, p<0.001) and hatchery-reared salmon (OR: 1.69 p=0.073) have higher odds of being PRV-infected than wild Atlantic salmon. Male salmon have double odds of being PRV infected compared to female salmon (OR: 2.11, p<0.001). Odds of being PRV-infected increased with body-length measured as decimetres (OR: 1.20, p=0.004). Since body length and sea-age are correlated (r=0.85 p<0.001), body length serves as a proxy for sea-age, meaning that spending more years in sea increases the odds of being PRV-infected.

Stochastic modelling of direct costs of pancreas disease (PD) in Norwegian farmed Atlantic salmon (Salmo salar L.).

An economic model for estimating the direct costs of disease in industrial aquaculture was developed to include the following areas: biological losses, extraordinary costs, costs of treatment, costs of prevention and insurance pay-out. Direct costs of a pancreas disease (PD) outbreak in Norwegian farmed Atlantic salmon were estimated in the model, using probability distributions for the biological losses and expenditures associated with the disease. The biological effects of PD on mortality, growth, feed conversion and carcass quality and their correlations, together with costs of prevention were established using elicited data from an expert panel, and combined with basal losses in a control model. Extraordinary costs and costs associated with treatment were collected through a questionnaire sent to staff managing disease outbreaks. Norwegian national statistics for 2007 were used for prices and production costs in the model. Direct costs associated with a PD-outbreak in a site stocked with 500,000 smolts (vs. a similar site without the disease) were estimated to NOK (Norwegian kroner) 14.4 million (5% and 95% percentile: 10.5 and 17.8) (NOK=euro0.12 or $0.17 for 2007). Production was reduced to 70% (5% and 95% percentile: 57% and 81%) saleable biomass, and at an increased production cost of NOK 6.0 per kg (5% and 95% percentile: 3.5 and 8.7).

Modelling sources of variation and risk factors for spinal deformity in farmed Atlantic salmon using hierarchical- and cross-classified multilevel models.

Sources of variation and risk factors for spinal deformity were investigated in a 2002-2004 year-class database of farmed Atlantic salmon using multilevel modelling. The prevalence of spinal deformity, recorded on subsamples of Atlantic salmon at individual days of harvest, was used as the outcome variable in the study. The dataset consisted of a multilevel structure with days of harvest (n=1441) nested within sea water pens (n=544), which were nested within sea water sites (n=39), which again were cross-classified with fresh water plants (n=21). A four level combined hierarchical- and cross-classified linear mixed model was built in MLwiN using Markov chain Monte Carlo (MCMC) estimation of variance components and fixed effects. Results revealed that a large part of the variance could be explained as sampling and classification random errors, accounting for 32% of the variation in the random intercept model and 41% of the variation in the final mixed effect model. Of the remaining "biological variation" in the random intercept model, 33% was explained by fixed effects where both the use half-year and 1.5 year old photo-manipulated autumn smolts (compared to using one year old spring smolt), and the use of six component vaccines (compared to using four and five component vaccines), were significantly associated with spinal deformity. The results suggest that the physiological changes at time of smoltification make Atlantic salmon susceptible to stressors causing vertebral deformation and that this is most evident in photo-manipulated fish smoltifying when temperature and growth is at its peak. The study further shows the potential of using multilevel modelling in epidemiological studies based on data from industrial aquaculture.