Molecular Epidemiological Investigation of Salmonid Alphavirus Genotype 2 (SAV2) Emergence on the Helgeland Coast of Norway in 2023

Abstract

Salmonid alphavirus (SAV) causes pancreas disease (PD) in Atlantic salmon and is a major viral pathogen affecting salmon aquaculture in Northern Europe. In Norway, PD is associated with genotypes SAV3 and marine SAV2, which have distinct geographical distributions. SAV3 predominates along the southwestern coast, whereas SAV2 has historically been restricted to Mid-Norway. In 2023, SAV2 was detected at four aquaculture sites along the Helgeland coast, north of the established PD zone, representing substantial northward expansion of the virus’ distribution. Whole-genome sequencing (WGS) provides high-resolution data for molecular epidemiological investigations and can distinguish between local viral persistence and recent introductions. In this study, nanopore-based WGS was applied to SAV2-positive samples collected from Norwegian aquaculture sites between 2017 and 2025. Genome sequences were analyzed with previously published Norwegian SAV2 sequences using Bayesian phylogenetic methods. Phylogenetic analyses estimated the most recent common ancestor of the Norwegian SAV2 lineage around 2006, indicating that the virus likely circulated in Norway for several years before its initial detection. SAV2 genomes from Helgeland showed high genetic similarity to genomes from sites within the PD zone, providing strong evidence of aquaculture-related spread. These findings demonstrate the value of WGS for tracing transmission pathways and supporting PD outbreak investigations.