Genomic analysis reveals low genetic diversity and no continuous reintroduction of piscine myocarditis virus in farmed Atlantic salmon in the Faroe Islands

Piscine myocarditis virus (PMCV) is the causative agent of cardiomyopathy syndrome (CMS), a significant disease in farmed Atlantic salmon (<i>Salmo salar</i> L.). Although an 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. Here, we present a fast amplicon-based whole-genome sequencing method of PMCV directly from field samples and disclose 48 novel genomes, adding to the single genome currently available. Phylogenetic analysis revealed that genomes with a broad spatiotemporal representation of Faroese farmed salmon formed a homogenous monophyletic cluster compared to 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. One genome from a returning wild salmon differed considerably from all the rest and formed an outgroup. All three ORFs exhibited signs of purifying selection, although ORF3 displayed a comparatively lower degree of selective constraint. Furthermore, no virulence-determining amino acid substitutions were identified in the Faroese genomes as no association was found between CMS cases and specific amino acid substitutions or motifs. Our data suggest that PMCV was introduced into the Faroe Islands from Norway, where brood fish is known to be infected. However, despite a steadily increasing import of Norwegian roe, our results show no continuous reintroduction of persisting PMCV strains to Faroese farmed salmon.