Sequencing and phylogenetic analysis was used to characterise a number of Scottish IPNV isolates. The majority of isolates from Scotland were genetically closely related to the Sp strain of IPNV. There appears to be a link between the IPN status of a farm and the presence of IPNV in the environment but this is short lived as IPNV does not typically persist in natural reservoirs at sufficiently high levels to allow re-infection to occur. Real-time PCR was used to study the expression of a subset of immune relevant genes following IPNV challenges by a natural (co-habitation) and unnatural (i.p.) route. Differences were observed between the two challenge routes which may reflect orientation towards a Th1 or Th2/regulatory response in i.p. and cohabiting infected fish respectively. These results may give us a better understanding of immune regulation in Atlantic salmon, and may lead to improved vaccine development. Real-time PCR was used to analyse the expression of the two Atlantic salmon IRF-1 isoforms, the results show that the IRF-1 gene is induced in response to IPNV infection in kidney tissue and in ASK cells but in macrophages no significant difference in expression was observed. SSH identified several candidate genes that may be part of a protection mechanism in Atlantic salmon important for controlling viral replication and the pathogenic effects of IPNV. Genes that were found to be significantly up-regulated belong functionally to the following groups of processes: proteolysis immune and stress response, transcription/replication, translation, protein transport/protein interactions and the metabolism. This is the first report identifying Vig-2 as being upregulated by IPNV.