Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

This work received support from the Biotechnology and Biological Sciences Research Council (grant BB/M010996/1) and Marine Scotland Science. The authors thank Dr Elena Fringuelli (Agri-Food and Biosciences Institute, Belfast) for providing some of the SAV material used.Peer reviewedPublisher PD

The economic benefits of disease triggered early harvest: a case study of pancreas disease in farmed Atlantic salmon from Norway

© 2015 Elsevier B.V. Pancreas disease (PD) is an important viral disease in Norwegian, Scottish and Irish aquaculture causing biological losses in terms of reduced growth, mortality, increased feed conversion ratio, and carcass downgrading. We developed a bio-economic model to investigate the economic benefits of a disease triggered early harvesting strategy to control PD losses. In this strategy, the salmon farm adopts a PCR (Polymerase Chain Reaction) diagnostic screening program to monitor the virus levels in stocks. Virus levels are used to forecast a clinical outbreak of pancreas disease, which then initiates a prescheduled harvest of the stock to avoid disease losses. The model is based on data inputs from national statistics, literature, company data, and an expert panel, and use stochastic simulations to account for the variation and/or uncertainty associated with disease effects and selected production expenditures. With the model, we compared the impacts of a salmon farm undergoing prescheduled harvest versus the salmon farm going through a PD outbreak. We also estimated the direct costs of a PD outbreak as the sum of biological losses, treatment costs, prevention costs, and other additional costs, less the costs of insurance pay-outs. Simulation results suggests that the economic benefit from a prescheduled harvest is positive once the average salmon weight at the farm has reached 3.2. kg or more for an average Norwegian salmon farm stocked with 1,000,000 smolts and using average salmon sales prices for 2013. The direct costs from a PD outbreak occurring nine months (average salmon weight 1.91. kg) after sea transfer and using 2013 sales prices was on average estimated at NOK 55.4 million (5%, 50% and 90% percentile: 38.0, 55.8 and 72.4) (NOK = €0.128 in 2013). Sensitivity analyses revealed that the losses from a PD outbreak are sensitive to feed- and salmon sales prices, and that high 2013 sales prices contributed to substantial losses associated with a PD outbreak

Controlling emerging infectious diseases in salmon aquaculture

In this paper, the authors review the impacts of diseases facing salmon aquaculture, drawing lessons from terrestrial animal diseases. They discuss the implementation of current control strategies, taking into account transmission patterns (vertical versus horizontal), disease reservoirs, and interactions with wild fish. In addition, the decision-making context of aquatic disease control and the institutional organisation of control strategies are considered, with particular emphasis on the roles and responsibilities of regulatory authorities and the private sector. Case studies on the emergence and control of infectious salmon anaemia worldwide and pancreas disease in Norway are used to examine some of the controversies that may influence decision making and provide lessons for the future

The epidemiological and economic effects from systematic depopulation of Norwegian marine salmon farms infected with pancreas disease virus

Pancreas disease (PD) is a viral disease associated with significant economic losses in Scottish, Irish, and Norwegian marine salmon aquaculture. In this paper, we investigate how disease-triggered harvest strategies (systematic depopulation of infected marine salmon farms) towards PD can affect disease dynamics and salmon producer profits in an endemic area in the southwestern part of Norway. Four different types of disease-triggered harvest strategies were evaluated over a four-year period (2011–2014), each scenario with different disease-screening procedures, timing for initiating the harvest interventions on infected cohorts, and levels of farmer compliance to the strategy. Our approach applies a spatio-temporal stochastic model for simulating the spread of PD in the separate scenarios. Results from these simulations were then used in cost-benefit analyses to estimate the net benefits of different harvest strategies over time. We find that the most aggressive strategy, in which infected farms are harvested without delay, was most efficient in terms of reducing infection pressure in the area and providing economic benefits for the studied group of salmon producers. On the other hand, lower farm compliance leads to higher infection pressure and less economic benefits. Model results further highlight trade-offs in strategies between those that primarily benefit individual producers and those that have collective benefits, suggesting a need for institutional mechanisms that address these potential tensions

Impacts of parasites on marine survival of Atlantic salmon: a meta-analysis

Parasites can, in theory, have large impacts on the survival of fish populations. One method to evaluate such impacts on anadromous species is to apply manipulative field experiments in which parallel groups of antiparasitically treated and non-treated fish are simultaneously released and then subsequently recaptured as returning adults. A systematic review and meta-analysis on all such Norwegian studies on Salmo salar provided a data set for the time period 1996 to 2011 on 118 release groups comprising 657 624 fish released and 3989 recaptured. The overall risk ratio (RR) was estimated to be 1.18 (95% CI: 1.07–1.30). The effect varied strongly between groups, (Higgins I2 = 40.1%). Over 70% of this heterogeneity could be explained by the release location, time period and baseline survival. The most important predictor variable was baseline survival. In groups with low recapture in the control group (low baseline survival), the effect of treatment was high (RR = 1.7), while in groups with high recapture in the control group (high baseline survival), there was no effect of treatment (RR ~ 1.00). The most prevalent parasite in the region affected by the drugs administered was Lepeophtheirus salmonis. Hence, the meta-analysis supports the hypothesis that L. salmonis contributes to the mortality of S. salar during outward migration. However, the effect of treatment was not consistent, but was evidently strongly modulated by other risk factors. The results suggest that the population-level effects of parasites cannot be estimated independently of other factors affecting the marine survival of S. salar. Emamectin benzoate, fish farming, Lepeophtheirus salmonis, parasite, salmon louse, substance E