Genetic diversity of piscine myocarditis virus in Atlantic salmon Salmo salar L. in Ireland

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.

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 (Salmo salar 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.

Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon

Over a decade since its discovery, piscine myocarditis virus (PMCV) remains a significant pathogen in Atlantic salmon aquaculture. Despite this significant impact, the genomic landscape, evolutionary dynamics, and virulence factors of PMCV are poorly understood. This study enhances the existing PMCV sequence dataset by adding 34 genome sequences and 202 new ORF3 sequences from clinical cardiomyopathy syndrome (CMS) cases in Norwegian aquaculture. Phylogenetic analyses, also including sequences from the Faroe Islands and Ireland revealed that PMCV sequences are highly conserved with distinct clustering by country of origin. Still, single CMS outbreaks display multiple PMCV variants, and although some clustering was seen by case origin, occasional grouping of sequences from different cases was also apparent. Temporal data from selected cases indicated increased sequence diversity in the population. We hypothesize that multiple bottlenecks and changing infection dynamics in the host population, with transfer to naïve individuals over time, represent a continuous selection pressure on the virus populations. No clear relation was found between PMCV variants and the severity of heart pathology. However, specific non-synonymous and synonymous mutations that might impact protein function and gene expression efficiency were identified. An additional factor that may impact PMCV replication is the presence of defective viral genomes, a novel finding for viruses of the order Ghabrivirales. This study provides new insights into PMCV genomic characteristics and evolutionary dynamics, highlighting the complex interplay of genetic diversity, virulence markers, and host-pathogen interactions, underscoring the epidemiological complexity of the virus. Keywords: piscine myocarditis virus; evolutionary dynamics; diversity; phylogeny; genomic sequencing; defective viral genomes.

Characterization of an outbreak of cardiomyopathy syndrome (CMS) in young Atlantic salmon, Salmo salar L

Cardiomyopathy syndrome (CMS) is the most common viral cardiac disease in Norwegian Atlantic salmon farming and typically affects large, market size fish. Only six months after seawater transfer, Atlantic salmon were diagnosed with CMS at a fish farm in the south-western part of Norway. Due to the unexpected young age and the remarkable large amounts of virus-specific RNA (Ct <10), the fish group was monitored with five additional samplings until slaughtered almost 10 months later. At three weeks after the first CMS diagnosis (weeks post-diagnosis, wpd) and at slaughter (39 wpd), more comprehensive samplings were performed of the study cage, with specific focus on three different cardiac compartments. The clinical, autopsy and histopathological findings at first diagnosis and at all succeeding samplings were similar to previous descriptions of typical CMS. A slightly elevated mortality was observed in the cage with diseased fish at the time of the first CMS diagnosis and continued throughout the study. The prevalence and load of PMCV-specific RNA in the fish remained high until slaughtering, with similar amounts in all sampled cardiac compartments. No fish from the other five cages at the site were diagnosed with CMS, until fish sampled from the last cage at the site were diagnosed 10 weeks after slaughtering of the study cage (49 wpd). Sequence analysis of the PMCV on the site showed that the outbreak virus was similar to PMCV variants previously sequenced from Norwegian field outbreaks. In conclusion, CMS in young Atlantic salmon had clinical signs and histopathological cardiac lesions typical for the disease, and diseased fish could be found in the study cage until slaughtering.

Data-Driven Network Modeling as a Framework to Evaluate the Transmission of Piscine Myocarditis Virus (PMCV) in the Irish Farmed Atlantic Salmon Population and the Impact of Different Mitigation Measures

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of Atlantic salmon caused by the piscine myocarditis virus (PMCV), which was first reported in Ireland in 2012. In this paper, we describe the use of data-driven network modeling as a framework to evaluate the transmission of PMCV in the Irish farmed Atlantic salmon population and the impact of different mitigation measures. Input data included live fish movement data from 2009 to 2017, population dynamics events and the spatial location of the farms. With these inputs, we fitted a network-based stochastic infection spread model. After assumed initial introduction of the agent in 2009, our results indicate that it took 5 years to reach a between-farm prevalence of 100% in late 2014, with older fish being most affected. Local spread accounted for only a small proportion of new infections, being more important for sustained infection in a given area. Spread via movement of subclinically infected fish was most important for explaining the observed countrywide spread of the agent. Of the targeted intervention strategies evaluated, the most effective were those that target those fish farms in Ireland that can be considered the most connected, based on the number of farm-to-farm linkages in a specific time period through outward fish movements. The application of these interventions in a proactive way (before the first reported outbreak of the disease in 2012), assuming an active testing of fish consignments to and from the top 8 ranked farms in terms of outward fish movement, would have yielded the most protection for the Irish salmon farming industry. Using this approach, the between-farm PMCV prevalence never exceeded 20% throughout the simulation time (as opposed to the simulated 100% when no interventions are applied). We argue that the Irish salmon farming industry would benefit from this approach in the future, as it would help in early detection and prevention of the spread of viral agents currently exotic to the country.