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Sequence data were generated for portions of the E2 and nsP3 genes of 48 salmonid alphaviruses from farmed Atlantic salmon (AS), Salmo salar L., and rainbow trout (RT), Oncorhynchus mykiss (Walbaum), in marine and freshwater environments, respectively, from the Republic of Ireland, Northern Ireland, England, Scotland, Norway, France, Italy and Spain between 1991 and 2007. Based on these sequences, and those of six previously published reference strains, phylogenetic trees were constructed using the parsimony method. Trees generated with both gene segments were similar. Clades corresponding to the three previously recognized subtypes were generated and in addition, two further new clades of viruses were identified. A single further strain (F96-1045) was found to be distinct from all of the other strains in the study. The percentage of nucleotide divergence within clades was generally low (0-4.8% for E2, 0-6.6% for nsP3). Interclade divergence tended to be higher (3.4-19.7% for E2, 6.5-28.1% for nsP3). Based on these results and using current SAV terminology, the two new clades and F96-1045 were termed SAV subtypes 4, 5 and 6, respectively. SAV4 contained AS strains from Ireland and Scotland, while SAV5 contained only Scottish AS strains. Recently identified SAV strains from RT in Italy and Spain were shown to belong to SAV2. In addition, marine AS strains belonging to SAV2 were identified for the first time. Analysis of the origin of several clusters of strains with identical E2 and nsP3 sequences strongly support horizontal transmission of virus between farms and aquaculture companies. Evidence in support of vertical transmission was not found.

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Infectious gill diseases of marine salmonid fish present a significant challenge in salmon-farming regions. Infectious syndromes or disease conditions affecting marine-farmed salmonids include amoebic gill disease (AGD), proliferative gill inflammation (PGI) and tenacibaculosis. Pathogens involved include parasites, such as Neoparamoeba perurans, bacteria, such as Piscichlamydia salmonis and Tenacibaculum maritimum, and viruses, such as the Atlantic salmon paramyxovirus (ASPV). The present level of understanding of these is reviewed with regard to risk factors, potential impacting factors, methods of best practice to mitigate infectious gill disease, as well as knowledge gaps and avenues for future research.

Gill disorders present a significant challenge in salmon (Salmo salar and Oncorhynchus sp.) farming regions throughout the world. This review of gill disorders and diseases of marine fish is focused on the non-infectious causes of gill disease in marine stage salmonids and these are grouped into harmful algae, such as Karenia mikimotoi, harmful zooplankton, such as Pelagia noctiluca, other environmental challenges, such as pollutants, as well as nutritional and genetic or congenital causes. The present level of understanding of these gill disorders is reviewed with regard to risk factors, potential impacting factors, methods of best practice to mitigate non-infectious gill disease and disorders, as well as knowledge gaps and avenues for future research.

Abstract. A rickettsia‐like organism was observed in tissues of farmed Atlantic salmon, Salmo salar L., experiencing mortalities in the West of Ireland. Gross pathology of affected fish included haemorrhages in the skeletal muscle, splenomegaly, congestion of pyloric caeca and yellow mottling of livers, which appeared in ring formations in some cases. Histopathology was most obvious in the spleens, livers, kidneys and hearts, with widespread tissue necrosis and numerous basophilic granules present in the cytoplasm and cytoplasmic vacuoles of a variety of cells. Transmission electron microscopy revealed micro‐organisms within membrane‐bound cytoplasmic vacuoles similar in appearance to rickettsia.

A description is given of cardiac and skeletal myopathy in Atlantic salmon, Sahno salar L., during pancreas disease. PosI-smoUs in two farms were sampled weekly from April to Oetober. Panereas disease was diagnosed at 9 and 13 weeks after sea transfer on the two farms, respeetively. Myodegenerative lesions were obser\'ed in the hearts of fish with hoth norma! and diseased panereas. The prevalenee of heart lesions was highest amongst fish affeetcd with panereas disease. Skeletal myopathy of red fibres was observed only in fish in the recovery and chronic phases of disease, whereas white fibre changes were observed in fish with normal pancreas and fish affeetcd with panereas disease.

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