Modelling temperature and fish biomass data to predict annual Scottish farmed salmon, Salmo salar L., losses: Development of an early warning tool.

Losses due to mortality are a serious economic drain on Scottish salmon aquaculture and are a limitation to its sustainable growth. Understanding the changes in losses, and associated drivers, are required to identify risks to sustainable aquaculture. Data on losses were obtained from two open source data sets: monthly losses of biomass 2003-2018 and losses of salmon over production cycles (numbers input minus output harvest) 2002-2016. Monthly loss rates increased, accelerating after 2010, while losses per production cycle displayed no trend. Two modelling frameworks were investigated to produce an early warning tool for managers about potential increases in losses. Both linear regression and beta regression showed that monthly losses related to biomass and minimum winter air temperatures with high precision and low bias. These relationships apply at both the national and regional levels where the beta regression best fit model explain 82 % and 69 % of variation in mortality, some regional differences apply, particularly for the Northern Isles. The lack of trend in losses per production cycle may have been due to shorter production cycles as more salmon were harvested earlier, and possibly increasing losses of larger salmon (which affects biomass but not numbers lost). In the long-term, the models predict that milder winters and increased biomass will be associated with increased mortality, which will need to be managed. In the short-term, given relatively little year-to-year variation in biomass, minimum winter temperature is a powerful early warning of the likely extent of losses in the Scottish salmon farming industry.

The contact structure of Great Britain's salmon and trout aquaculture industry.

We analyse the network structure of the British salmonid aquaculture industry from the perspective of infectious disease control. We combine for the first time live fish transport (or movement) data covering England and Wales with data covering Scotland and include network layers representing potential transmission by rivers, sea water and local transmission via human or animal vectors in the immediate vicinity of each farm or fishery site. We find that 7.2% of all live fish transports cross the England-Scotland border and network analysis shows that 87% of English and Welsh nodes and 72% of Scottish nodes are reachable from cross-border connections via live fish transports alone. Consequently, from a disease-control perspective, the contact structures of England and Wales and of Scotland should not be considered in isolation. We also show that large epidemics require the live fish movement network and so control strategies targeting movements can be very effective. While there is relatively low risk of widespread epidemics on the live fish transport network alone, the potential risk is substantially amplified by the combined interaction of multiple network layers.

A survey of wild marine fish identifies a potential origin of an outbreak of viral haemorrhagic septicaemia in wrasse, Labridae, used as cleaner fish on marine Atlantic salmon, Salmo salar L., farms.

Viral haemorrhagic septicaemia virus (VHSV) was isolated from five species of wrasse (Labridae) used as biological controls for parasitic sea lice predominantly, Lepeophtheirus salmonis (Krøyer, 1837), on marine Atlantic salmon, Salmo salar L., farms in Shetland. As part of the epidemiological investigation, 1400 wild marine fish were caught and screened in pools of 10 for VHSV using virus isolation. Eleven pools (8%) were confirmed VHSV positive from: grey gurnard, Eutrigla gurnardus L.; Atlantic herring, Clupea harengus L.; Norway pout, Trisopterus esmarkii (Nilsson); plaice, Pleuronectes platessa L.; sprat, Sprattus sprattus L. and whiting, Merlangius merlangus L. The isolation of VHSV from grey gurnard is the first documented report in this species. Nucleic acid sequencing of the partial nucleocapsid (N) and glycoprotein (G) genes was carried out for viral characterization. Sequence analysis confirmed that all wild isolates were genotype III the same as the wrasse and there was a close genetic similarity between the isolates from wild fish and wrasse on the farms. Infection from these local wild marine fish is the most likely source of VHSV isolated from wrasse on the fish farms.

An approach to evaluating the reliability of diagnostic tests on pooled groups of infected individuals.

An experimental design and statistical analysis providing information on the reliability of pooled test procedures is described. It involves estimating the relationship between the probability of a positive pooled test result (dependent variable) and the expected number of infected individuals in a pool (explanatory variable). The intercept is an estimate of the proportion of false positives (1-pooled specificity) and pooled sensitivities can be estimated for indicative prevalences of infected individuals. Simulations for a theoretical infection are used to investigate the advantages and limitations of the approach. The approach is used to evaluate the reliability of a virus isolation and qRT-PCR test procedure detecting Salmonid alphavirus the pathogenic agent necessary for the development of Pancreas Disease in Atlantic salmon (Salmo salar).

The potential for targeted surveillance of live fish movements in Scotland.

The network structure of the movements of live fish in the Scottish aquaculture industry has recently been demonstrated for 2003. In this paper, we enlarge this analysis to a longer 3-year period from 2002 to 2004, the new data allowing complete coverage of at least one production cycle. The resulting network contains slightly more sites than that for a single year and is denser with more arcs (directed site-to-site connections) present, but otherwise features recognizable in the 1-year network are still recognizable in the 3-year network. Arc-removal algorithms (a proxy for targeted surveillance) were identified that could successfully reduce the portion of the network reachable from a node (a proxy for potential epidemic size) by approximately one-third by removing as few as four arcs. This results from the high centrality of particular nodes and arcs. A strong community structure was identified in the network, corresponding with species farmed, but only weakly geographical, with a high proportion of arcs occurring between management areas and catchments.

Seasonality and heterogeneity of live fish movements in Scottish fish farms.

Movement of live animals is a key contributor to disease spread. Farmed Atlantic salmon Salmo salar, rainbow trout Onchorynchus mykiss and brown/sea trout Salmo trutta are initially raised in freshwater (FW) farms; all the salmon and some of the trout are subsequently moved to seawater (SW) farms. Frequently, fish are moved between farms during their FW stage and sometimes during their SW stage. Seasonality and differences in contact patterns across production phases have been shown to influence the course of an epidemic in livestock; however, these parameters have not been included in previous network models studying disease transmission in salmonids. In Scotland, farmers are required to register fish movements onto and off their farms; these records were used in the present study to investigate seasonality and heterogeneity of movements for each production phase separately for farmed salmon, rainbow trout and brown/sea trout. Salmon FW-FW and FW-SW movements showed a higher degree of heterogeneity in number of contacts and different seasonal patterns compared with SW-SW movements. FW-FW movements peaked from May to July and FW-SW movements peaked from March to April and from October to November. Salmon SW-SW movements occurred more consistently over the year and showed fewer connections and number of repeated connections between farms. Therefore, the salmon SW-SW network might be treated as homogeneous regarding the number of connections between farms and without seasonality. However, seasonality and production phase should be included in simulation models concerning FW-FW and FW-SW movements specifically. The number of rainbow trout FW-FW and brown/sea trout FW-FW movements were different from random. However, movements from other production phases were too low to discern a seasonal pattern or differences in contact pattern.

An experimental investigation on aspects of infectious salmon anaemia virus (ISAV) infection dynamics in seawater Atlantic salmon, Salmo salar L.

This study investigated infection dynamics of infectious salmon anaemia virus (ISAV) by conducting two experiments to examine minimum infective dose and viral shedding of ISAV. In terms of minimum infective dose, the high variability between replicate tanks and the relatively slow spread of infection through the population at 1 x 10(1) TCID(50) mL(-1) indicated this dose is approaching the minimum infective dose for ISAV in seawater salmon populations. A novel qPCR assay incorporating an influenza virus control standard with each seawater sample was developed that enabled the quantity of ISAV shed from infected populations to be estimated in values equivalent to viral titres. Viral shedding was first detected at 7 days post-challenge (5.8 x 10(-2) TCID(50) mL(-1)kg(-1)) and rose to levels above the minimum infective dose (4.2 x 10(1) TCID(50) mL(-1)kg(-1)) on day 11 post-challenge, 2 days before mortalities in ISAV inoculated fish started. These results clearly demonstrate that a large viral shedding event occurs before death. Viral titres peaked at 7.0 x 10(1) TCID(50) mL(-1)kg(-1) 15 days post-infection. These data provide important information relevant to the management of ISA.

Estimation of infectious dose and viral shedding rates for infectious pancreatic necrosis virus in Atlantic salmon, Salmo salar L., post-smolts.

Infectious dose and shedding rates are important parameters to estimate in order to understand the transmission of infectious pancreatic necrosis virus (IPNV). Bath challenge of Atlantic salmon post-smolts was selected as the route of experimental infection as this mimics a major natural route of exposure to IPNV infection. Doses ranging from 10(2) to 10(-4) 50% end-point tissue culture infectious dose (TCID(50)) mL(-1) sea water were used to estimate the minimum infectious dose for a Scottish isolate of IPNV. The minimum dose required to induce infection in Atlantic salmon post-smolts was <10(-1) TCID(50) mL(-1) by bath immersion (4 h at 10 degrees C). The peak shedding rate for IPNV following intraperitoneal challenge using post-smolts was estimated to be 6.8 x 10(3) TCID(50) h(-1) kg(-1) and occurred 11 days post-challenge. This information may be incorporated into mathematical models to increase the understanding of the dispersal of IPNV from marine salmon sites.

Detection of infectious pancreatic necrosis virus (IPNV) from the environment in the vicinity of IPNV-infected Atlantic salmon farms in Scotland.

Infectious pancreatic necrosis virus (IPNV) has been isolated from mussels, sediment and surface water in the vicinity of clinically infected salmon farms, at shore bases supplying the farms and for several hundred metres distance from farms in the direction of current flow. There was evidence of decreasing prevalence of IPNV in mussels from Shetland once IPN outbreaks subsided, indicating they are an unlikely source of re-infection on farms. There was little evidence of persistence in the environment, although conclusions were complicated by the presence of IPNV on neighbouring farms 1 year after the outbreak.

Training needs analysis within the community.

A project was undertaken to provide a description of the training needs of agencies who are partners in the provision of care in the community. In developing the research strategy a service design approach was adopted which complied with the design control requirement of the Quality Standard EN ISO 9001: 1994. A questionnaire for self-completion was sent to 25 individuals involved in delivering community care. The findings enabled priorities of joint training to be identified. The findings also enabled training to be suggested for both manager and direct care staff. Demonstrates the need for skill acquisition in a variety of areas. Generally it was indicated by respondents that planning training arising from the project should be multidisciplinary. Enthusiasm for such training was also a feature of the respondents' responses.