Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland

Piscine myocarditis virus (PMCV), a double-stranded RNA virus, is the causative agent of cardiomyopathy syndrome (CMS) in Atlantic salmon Salmo salar, which was first reported in Ireland in 2012. PMCV continues to be a disease threat to Atlantic salmon aquaculture in Ireland, and as such, it is of growing importance to understand how the virus spreads. Genetic sequences allow for transmission pathways to be examined, with whole genomes providing the most accurate information. In this study, whole genome sequencing has been applied to Irish strains of PMCV, in doing so revealing how > 80% of the genetic diversity of the virus lies outside the commonly sequenced open reading frames (ORFs). Second, this paper examines the effectiveness of incorporating a MinION sequencing approach into routine diagnostics by comparing a MinION generated genome to the corresponding sequence generated via Illumina MiSeq. The results showed the MinION genome shared 99.59% identity with the Illumina genome, and while this accuracy may be sufficient for studies such as pathogen identification and deeper evolutionary questions, it was shown to be insufficient for accurately tracking viral transmission pathways. Finally, comparing Irish and Faroese sequences reveals that some strains of PMCV in Ireland may originate from wild fish.