Salmon pancreas disease virus, an alphavirus infecting farmed Atlantic salmon, Salmo salar L.

A 5.2-kb region at the 3' terminus of the salmon pancreas disease virus (SP DV) RNA genome has been cloned and sequenced. The nucleotide and predicted amino acid sequences show that SPDV shares considerable organizational and sequence identity to members of the genus alphavirus within the family Toga viridae. The SPDV structural proteins encoded by the 5.2-kb region contain a number of unique features when compared to other sequenced alphaviruses. Based on cleavage site homologies, the predicted sizes of the SPDV envelope glycoproteins E2 (438 aa) and E1. (461 aa) are larger than those of other alphaviruses, while the predicted size of the alphavirus 6K protein is 3.2 K (32 aa) in SPDV. The E2 and E1 proteins each carry one putative N-linked glycosylation site, with the site in E1 being found at a unique position. F rom amino acid sequence comparisons of the SPDV structural region with sequ enced alphaviruses overall homology Is uniform, ranging from 32 to 33%. Whi le nucleotide sequence analysis of the 26S RNA junction region shows that S PDV is similar to other alphaviruses, analysis of the 3'-nontranslated regi on reveals that SPDV shows divergence in this region. (C) 1999 Academic Pre ss.