Prospective longitudinal studies of two outbreaks of pancreas disease in Atlantic salmon (AS), Salmo salar L., in Ireland were conducted. Both outbreaks occurred during the marine phase of production, with one caused by salmonid alphavirus subtype 1 (SAV1) and the other by SAV4. In addition to screening a range of tissues by real-time reverse transcriptase polymerase chain reaction (RRT-PCR), virological, serological and histopathological examinations were performed along with partial genome sequencing and results were related to environmental and production data and farm history. On Farm 1 (marine sampling only), infection was detected within 3 weeks of smolts being placed on the farm, while on Farm 2 (freshwater and marine sampling), infection was first detected 315 days after transfer to sea. In both outbreaks, RRT-PCR signals were detected in a range of tissues including gill, heart, kidney, pancreas/pyloric caeca, brain and serum. Persistence of signal was longest in gill and heart (> or =265 days on both farms) and shortest in serum. Mortalities on the two farms varied from 10.9% to 30%. In both cases, partial genome sequence of the causative viruses were identical to SAV strains detected in previous populations of AS on each of the study farms, including populations with which the study populations overlapped in time and space.

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Infectious pancreatic necrosis is a significant disease of farmed salmonids resulting in direct economic losses due to high mortality and disease-management costs. Significant outbreaks of the disease occurred in farmed Atlantic salmon in Ireland between 2003 and 2007, associated with imported ova and smolts. As the virus was known to occur in the country since the development of aquaculture in the 1980s, this study examined archived samples to determine whether these older isolates were associated with virulent forms. The study showed that two genotypes of IPNV were present in the 1990s, genotype 3 and genotype 5. A more virulent subtype of the virus first appeared in 2003 associated with clinical outbreaks of IPN, and this subtype is now the most prevalent form of IPNV found in the country. The data also indicated that IPNV in Ireland is more closely related to Scottish and continental European isolates than to Norwegian, Chilean and Australasian genogroup 5 isolates.

Rhabdovirus infections are an emerging problem for both wild and farmed freshwater fish in Northern Europe. In October 2005, a clinical outbreak with an approximate mortality rate of 40% occurred in a single batch of juvenile perch on a farm in the Republic of Ireland. Clinical signs developed slowly and were consistent with a perch rhabdovirus infection: signs included haemorrhages at the base of the fins and apparent impairment of the central nervous system (manifested as loss of equilibrium and erratic swimming behaviour). Studies suggest that the infected fish originated from a hatchery within the country which relied on wild fish broodstock to supplement the production of perch juveniles. A related rhabdovirus was subsequently isolated from this hatchery. Virus isolation studies have shown that rhabdoviruses were often isolated from wild fish in the vicinity of the hatchery between 1993 and 2005. All isolates were analysed using a generic primer set specific for the L gene of fish vesiculotype viruses. Phylogenetic analysis revealed that all isolates recovered from perch clustered together with the European lake trout rhabdovirus (903/87) of the genus Perhabdovirus. In addition to this, anguillid rhabdovirus was isolated from eel, and the partial L-gene sequence of a previously reported isolate from tench clustered with the pike fry rhabdoviruses, in the genus Sprivivirus.

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