Cardiomyopathy syndrome (CMS): An emerging risk factor for Faroese Atlantic salmon aquaculture?

Piscine myocarditis virus (PMCV) is the causative agent of cardiomyopathy syndrome (CMS), a significant disease in farmed Atlantic salmon (Salmo salar L.). Although increasing number of CMS outbreaks have been recorded in the Faroe Islands since the reemergence of CMS in 2013, overall PMCV genetic diversity, transmission pathways and evolutionary trajectories remain elusive. There is currently no way of cultivating the virus and only one whole genome has been publicly available.

Here we present a fast amplicon-based whole genome sequencing method of PMCV directly from field samples. Phylogenetic analysis of 48 high-quality novel PMCV genomes with a broad spatiotemporal representation of farmed salmon demonstrated that the Faroese PMCV strains formed a monophyletic cluster when compared with Norwegian and Irish PMCV genomes. Homogeneity of the Faroese genomes was substantiated with principal component analyses, where no spatiotemporal clustering of genotypes was found, nor any clustering based on roe or smolt origin. However, the PMCV genome from a returning wild salmon differed considerably from all the rest and formed an outgroup. All three open reading frames (ORFs) exhibited evidence of purifying selection, although ORF3 displayed a comparatively lower degree of selective constraint. Furthermore, no virulence-determining mutations were identified in the Faroese genomes as no association was found between assigned CMS cases and specific amino acid substitutions or motifs. Our data suggests that PMCV was introduced into the Faroe Islands from Norway. However, despite a steadily increasing import of Norwegian roe, our results show no continuous reintroduction of persistent PMCV strains to Faroese farmed salmon but local spread of PMCV between the farming sites.