Short report

Characterization of untranslated regions of the salmonid alphavirus 3 (SAV3) genome and construction of a SAV3 based replicon

Marius Karlsen¹ , Stephane Villoing² , Espen Rimstad³ and Are Nylund¹

¹  Department of Biology, University of Bergen, Thor Møhlens gate 55, 5020 Bergen, Norway

²  Intervet Norbio, Thor Møhlens gate 55, 5008 Bergen, Norway

³  Norwegian School of Veterinary Science, Oslo, Norway

author email corresponding author email

Virology Journal 2009, 6:173doi:10.1186/1743-422X-6-173

Published:	27 October 2009

Abstract

Salmonid alphavirus (SAV) causes disease in farmed salmonid fish and is divided into different genetic subtypes (SAV1-6). Here we report the cloning and characterization of the 5'- and 3'- untranslated regions (UTR) of a SAV3 isolated from Atlantic salmon in Norway. The sequences of the UTRs are very similar to those of SAV1 and SAV2, but single nucleotide polymorphisms are present, also in the 3' - conserved sequence element (3'-CSE). Prediction of the RNA secondary structure suggested putative stem-loop structures in both the 5'- and 3'-ends, similar to those of alphaviruses from the terrestrial environment, indicating that the general genome replication initiation strategy for alphaviruses is also utilized by SAV. A DNA replicon vector, pmSAV3, based upon a pVAX1 backbone and the SAV3 genome was constructed, and the SAV3 non-structural proteins were used to express a reporter gene controlled by the SAV3 subgenomic promoter. Transfection of pmSAV3 into CHSE and BF2 cell lines resulted in expression of the reporter protein, confirming that the cloned SAV3 replication apparatus and UTRs are functional in fish cells.