The use of Taqman real-time PCR-based technology has recently become more frequent in the detection of pathogens in the aquaculture industry. This interest has necessitated the development of robust and reliable pathogen-detection assays. The development of a range of endogenous control assays to be run alongside these diagnostic assays works to further increase confidence in the latter. This study describes the design of a range of endogenous control assays based on the elongation factor 1-α (EF1-α) gene specific to a range of fish species including Atlantic salmon, Salmo salar; rainbow trout, Oncorhynchus mykiss; brown trout, Salmo trutta; cod, Gadus morhua; haddock, Melanogrammus aeglefinus; saithe, Pollachius virens; whiting, Merlangius merlangus; Norway pout, Trisopterus esmarkii; carp (family Cyprinidae), roach, Rutilus rutilus; European eel, Anguilla anguilla; and herring, Clupea harengus, as well as a number of fish cell lines. Evidence is provided of the validation of these assays for specific species, a range of tissue types and cell lines as well as an example of the potential uses of these assays.

Surveillance data on the distribution of viral haemorrhagic septicaemia virus (VHSV) in the North Sea (UK), targeting Atlantic herring in areas with previous virus detection, were obtained from research cruises conducted during 2005. The sensitive molecular approach of real-time RT-PCR (qRT-PCR) was applied alongside a newly developed endogenous positive control assay specific for herring (elongation factor 1α) to ensure integrity of template. Three hundred and five pools from 1937 individual herring were tested, and no evidence of VHSV in association with wild Atlantic herring was detected. Samples were obtained from Scottish waters where marine aquaculture is conducted. The results confirm that previous tissue culture studies have most likely not significantly underestimated the prevalence of carrier herring in this area. The significance of migratory species such as herring as a reservoir species for VHSV, with the potential to translocate virus genotypes between geographical areas, is discussed.

A large proportion of the European population of harbor seals (Phoca vitulina) live around the British coastline. Numbers of harbor seal have been decreasing at the majority of breeding sites around Britain (Lonergan et al. 2007). This decline may be caused by a number of different factors such as disease, changes in prey availability, environmental contamination (Hall et al. 2006), competition with gray seals (Halichoerus grypus), or a combination of different drivers . In order to investigate factors linked to changes in the availability of prey, including competition with gray seals, information on the seal diet is required. Analysis of prey remains recovered from scat is often used to determine the diet of pinnipeds. This methodology is both noninvasive and allows large sample sizes to be collected (Pierce et al. 1991). Scat are often collected from mixed species haul-out sites that are used by both harbor and gray seals. Previous work in the Moray Firth, UK, has shown that 15% of gray seal scat samples were misidentified as belonging to harbor seals (Reed et al. 1997), while other studies have reported even higher level of misidentification (Masland et al. 2010). As scat from the two species are visually indistinguishable, it has not been possible to investigate the dietary overlap, and hence the potential for competition, between sympatric populations of the two seal species. Conclusions drawn from samples collected at separate sites, or times, are confounded by known spatial and temporal variation in diet (Hammond et al. 1994, Tollit and. A recent study described the use of conventional polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis to discriminate between harbor and gray seal scat (Masland et al. 2010), while other studies have used allele frequency distribution from microsatellite analysis to identify scat from these species (Reed et al. 1997).Previous studies have reported differences in foraging behavior of male and female harbor and gray seals which may result in differences in their diet (Thompson et al. 1998, Beck et al. 2007. Therefore, knowledge of the sex of the animals producing different scat samples is required in order to accurately characterize seal diet. Sex

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Salmon pancreas disease virus is an alphavirus (family Togaviridae) affecting mainly Atlantic salmon (Salmo salar L.). Both polyprotein sequences of the Scottish isolate (SAV4640) were determined and compared with those of Irish isolate SAVF93-125. High amino acid sequence similarity (99.4 %) was found. Six amino acid deletions were found in the E2 gene of SAV4640. SAVF93-125 demonstrated a high viral load in culture despite high Mx expression. Approximately 50 % of cells infected with SAVF93-125 exhibited a cytopathic effect by day 8. SAV4640 successfully entered the cells, inducing 10,500-fold higher Mx expression at day 2 compared to SAVF93-25; however, no replication was observed based on results of the nsP1 qRT-PCR.