05 ml/fish), a commercial monovalent SAV vaccine (0.1 ml/fish), a placebo adjuvant vaccine (0.1 ml/fish) or PBS (0.1 ml/fish). After a six weeks smoltification period, the fish were distributed to duplicate tanks with seawater. The fish that were to be evaluated in the i.p. injection model, and that served as shedders for the fish in the cohabitation model, were then challenged with the isolate ALV413 at a final dose of 1.15 × 108 TCID50/fish. Samples from heart, pancreas and skeletal muscle were taken for histological analysis from all cohabitant groups 3–5 weeks post challenge (n = 10 per

tank/20 per group, per time point, unless otherwise stated). Heart-tissues were also stored on RNA-later (Ambion) and used for RNA extraction and PCR analyses. Sera were collected from the caudal vein for evaluation of viraemia by isolation of infectious virus in GW-572016 price Chum salmon heart (CHH) cells using previously described techniques [18] and [19]. Samples were also taken from surviving fish in the i.p. challenged groups four weeks p.i. (n = 5 per tank/10 per group, except for in the PBS placebo group where n = 4 and 2 from the two tanks due to few survivors). Tissues were fixed in 10% phosphate-buffered formalin for a minimum of 48 h prior to being submitted

blinded to the Norwegian Veterinary Institute, Oslo, Norway for embedment in paraffin wax, sectioning at 4–5 μm and staining with hematoxylin and eosin according to their standard procedure. Blinded slides were scored for lesion severity using a visual analogous scale as previously described [17] (Supplementary Table 1). Heart Apoptosis Compound Library manufacturer samples were collected aseptically without penetrating the peritoneal cavity, stored on RNAlater and submitted to an accredited commercial laboratory for RNA extraction and Real-Time PCR analyses (PatoGen Analyse AS, Ålesund, Norway). The returned results were treated as positive/negative, or semi-quantitative. In the latter case, raw Ct-values that were obtained with a previously

described Taqman assay targeting the coding sequence of SAV nsP1 [20] were normalized against the Ct-values from an assay targeting the mRNA of cellular elongation factor 1a [21] using the Q-gen software [22]. PCR efficiencies these for the two assays were provided by PatoGen Analyse AS for inclusion in the analysis (slopes = −3.25 for SAV and −3.41 for ElA). Normalized Ct-values were divided by the lowest value in the groups compared and Log2 transformed for presentation. The trial included two cages of Atlantic salmon (Cage 1: n = 109 203, cage 2: n = 126 254), held under industrial conditions at a commercial seawater fish farm in Western Norway. All the fish were of the same strain and origin and were vaccinated in the freshwater stage (January 11th–February 3rd, 2011) with the commercial multi-component vaccine ALPHA JECT micro®6, that does not contain any SAV antigens.