First detection of Ichthyophonus sp. in invasive wild pink salmon (Oncorhynchus gorbuscha) from the North Atlantic Ocean.

Pacific pink salmon (Oncorhynchus gorbuscha) were deliberately introduced to rivers surrounding the White Sea and has spread to Norway and several other countries surrounding the North Atlantic Ocean. In August 2021, a female pink salmon displaying pale gills and abnormal behaviour was captured in River Lakselva in Northern Norway and later submitted to the Norwegian Veterinary Institute (NVI) for post-mortem examination. Histological examination of organ samples revealed structures indicative of systemic ichthyophoniasis, caused by Ichthyophonus sp. The parasites appeared to be especially abundant in the heart and skeletal musculature, and local tissue responses were assessed to be absent or very mild. Sequences of the ribosomal 18S rRNA and the mitochondrial cytochrome oxidase 1 (CO1) genes confirmed the diagnosis and identified the pathogen as Ichthyophonus sp. The CO1 sequence further established that the isolate from pink salmon was most similar to sequences of Ichthyophonus sp. from Atlantic salmon, Salmo salar, from the Atlantic Ocean on the east coast of the US and from Atlantic herring, Clupea harengus, from Iceland. We here report the first detection of Ichthyophonus sp. in pink salmon in the North Atlantic Ocean.

Genotyping of Salmon Gill Poxvirus Reveals One Main Predominant Lineage in Europe, Featuring Fjord- and Fish Farm-Specific Sub-Lineages.

Salmon gill poxvirus (SGPV) can cause serious gill disease in Atlantic salmon (Salmo salar L.) and represents a significant problem to aquaculture industries in Northern Europe. Here, a single-tube multi-locus variable-number tandem-repeat (VNTR) analysis (MLVA) genotyping assay, targeting eight VNTR loci, was developed for studying the epizootiology of SGPV. Through MLVA typing of SGPV positive samples from 180 farmed and wild Atlantic salmon in Northern Europe, the first molecular population study of this virus was undertaken. Comparison of resulting MLVA profiles by cluster analysis revealed considerable micro-diversity, while only a limited degree of specific clustering by country of origin could be observed, and no clustering relating to the severity of disease outbreaks. Phylogenetic analysis, based on genomic data from six SGPV specimens (three Norwegian, one Scottish, one Faroese and one Canadian), complemented and corroborated MLVA by pointing to a marked transatlantic divide in the species, with one main, relatively conserved, SGPV lineage as predominant in Europe. Within certain fjord systems and individual freshwater salmon smolt farms in Norway, however, discrete MLVA clustering patterns that prevailed over time were observed, likely reflecting local predominance of specific SGPV sub-lineages. MLVA typing was also used to refute two suspected instances of vertical SGPV transmission from salmon broodstock to offspring, and to confirm a failed disinfection attempt in one farm. These novel insights into the previously undocumented population structure of SGPV provide important clues, e.g., regarding the mechanisms underlying spread and recurrence of the virus amongst wild and farmed salmon populations, but so far no indications of more or less virulent SGPV sub-lineages have been found. The MLVA scheme represents a highly sensitive genotyping tool particularly well suited for illuminating SGPV infection routes, and adds to the relatively low number of MLVA protocols that have so far been published for viral species. Typing is reasonably inexpensive, with a moderate technological requirement, and may be completed within a single working day. Resulting MLVA profiles can be readily shared and compared across laboratories, facilitating rapid placement of samples in an international ezpizootiological context.

Correction to: An Illumina approach to MHC typing of Atlantic salmon.

The original version of this article was published without open access. With the author(s)' decision to opt for Open Choice the copyright of the article changed.

An Illumina approach to MHC typing of Atlantic salmon.

The IPD-MHC Database represents the official repository for non-human major histocompatibility complex (MHC) sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. IPD-MHC gathers allelic MHC class I and class II sequences from classical and non-classical MHC loci from various non-human animals including pets, farmed and experimental model animals. So far, Atlantic salmon and rainbow trout are the only teleost fish species with MHC class I and class II sequences present. For the remaining teleost or ray-finned species, data on alleles originating from given classical locus is scarce hampering their inclusion in the database. However, a fast expansion of sequenced genomes opens for identification of classical loci where high-throughput sequencing (HTS) will enable typing of allelic variants in a variety of new teleost or ray-finned species. HTS also opens for large-scale studies of salmonid MHC diversity challenging the current database nomenclature and analysis tools. Here we establish an Illumina approach to identify allelic MHC diversity in Atlantic salmon, using animals from an endangered wild population, and alter the salmonid MHC nomenclature to accommodate the expected sequence expansions.

Pancreas disease caused by Salmonid alphavirus subtype 2 reduces growth and feed conversion in farmed Atlantic salmon.

Pancreas disease (PD), caused by several subtypes of salmonid alphavirus (SAV), is associated with significant economic losses in European salmonid aquaculture. In this retrospective cohort study, we investigate the impact of PD caused by SAV subtype 2 (SAV2) on growth, feed conversion, and mortality in farmed Atlantic salmon (Salmo salar L.). The study was based on harvest data from a large salmon farming company operating in the SAV2 endemic area of Norway. Mixed-effect regression analyses showed a severe impact on both growth and feed conversion when PD appeared late in the production cycle. In a scenario with fixed slaughter time the estimated impact corresponded to a growth reduction of 0.7 kg and 0.07 points increase in feed conversion ratio. No effect on mortality was observed in this data set. In conclusion, the most important consequences of PD caused by SAV2 infection is reduced growth and feed conversion in large Atlantic salmon. The lack of effect on mortality in this study may be due to other factors overshadowing the impact of PD.

Piscine orthoreovirus-3 is prevalent in wild seatrout (Salmo trutta L.) in Norway.

In 2017, a PCR-based survey for Piscine orthoreovirus-3 (PRV-3) was conducted in wild anadromous and non-anadromous salmonids in Norway. In seatrout (anadromous Salmo trutta L.), the virus was present in 16.6% of the fish and in 15 of 21 investigated rivers. Four of 221 (1.8%) Atlantic salmon (Salmo salar L.) from three of 15 rivers were also PCR-positive, with Ct-values indicating low amounts of viral RNA. All anadromous Arctic char (Salvelinus alpinus L.) were PCR-negative. Neither non-anadromous trout (brown trout) nor landlocked salmon were PRV-3 positive. Altogether, these findings suggest that in Norway PRV-3 is more prevalent in the marine environment. In contrast, PRV-3 is present in areas with intensive inland farming in continental Europe. PRV-3 genome sequences from Norwegian seatrout grouped together with sequences from rainbow trout (Oncorhynchus mykiss Walbaum) in Norway and Coho salmon (Oncorhynchus kisutch Walbaum) in Chile. At present, the origin of the virus remains unknown. Nevertheless, the study highlights the value of safeguarding native fish by upholding natural and artificial barriers that hinder introduction and spread, on a local or national scale, of alien fish species and their pathogens. Accordingly, further investigations of freshwater reservoirs and interactions with farmed salmonids are warranted.

Effect of pancreas disease caused by SAV 2 on protein and fat digestion in Atlantic salmon.

Salmonid alphavirus (SAV) causes pancreas disease (PD) in farmed Atlantic salmon (Salmo salar L.), and exocrine pancreas tissue is a primary target of the virus. Digestive enzymes secreted by the exocrine pancreas break down macromolecules in feed into smaller molecules that can be absorbed. The effect of SAV infection on digestion has been poorly studied. In this study, longitudinal observations of PD outbreaks caused by SAV subtype 2 (SAV2) in Atlantic salmon at two commercial sea sites were performed. The development of PD was assessed by measurement of SAV2 RNA load and evaluation of histopathological lesions typical of PD. Reduced digestion of both protein and fat co-varied with the severity of PD lesions and viral load. Also, the study found that during a PD outbreak, the pen population comprise several subpopulations, with different likelihoods of being sampled. The body length of sampled fish deviated from the expected increase or steady state over time, and the infection status in sampled fish deviated from the expected course of infection in the population. Both conditions indicate that disease status of the individual fish influenced the likelihood of being sampled, which may cause sampling bias in population studies.

Phylogenetic evidence of long distance dispersal and transmission of piscine reovirus (PRV) between farmed and wild Atlantic salmon.

The extent and effect of disease interaction and pathogen exchange between wild and farmed fish populations is an ongoing debate and an area of research that is difficult to explore. The objective of this study was to investigate pathogen transmission between farmed and wild Atlantic salmon (Salmo salar L.) populations in Norway by means of molecular epidemiology. Piscine reovirus (PRV) was selected as the model organism as it is widely distributed in both farmed and wild Atlantic salmon in Norway, and because infection not necessarily will lead to mortality through development of disease. A matrix comprised of PRV protein coding sequences S1, S2 and S4 from wild, hatchery-reared and farmed Atlantic salmon in addition to one sea-trout (Salmo trutta L.) was examined. Phylogenetic analyses based on maximum likelihood and Bayesian inference indicate long distance transport of PRV and exchange of virus between populations. The results are discussed in the context of Atlantic salmon ecology and the structure of the Norwegian salmon industry. We conclude that the lack of a geographical pattern in the phylogenetic trees is caused by extensive exchange of PRV. In addition, the detailed topography of the trees indicates long distance transportation of PRV. Through its size, structure and infection status, the Atlantic salmon farming industry has the capacity to play a central role in both long distance transportation and transmission of pathogens. Despite extensive migration, wild salmon probably play a minor role as they are fewer in numbers, appear at lower densities and are less likely to be infected. An open question is the relationship between the PRV sequences found in marine fish and those originating from salmon.

Associations between piscine reovirus infection and life history traits in wild-caught Atlantic salmon Salmo salar L. in Norway.

Piscine Reovirus (PRV), the putative causative agent of heart and skeletal muscle inflammation (HSMI), is widely distributed in both farmed and wild Atlantic salmon (Salmo salar L.) in Norway. While HSMI is a common and commercially important disease in farmed Atlantic salmon, the presence of PRV has so far not been associated with HSMI related lesions in wild salmon. Factors associated with PRV-infection were investigated in returning Atlantic salmon captured in Norwegian rivers. A multilevel mixed-effect logistic regression model confirmed clustering within rivers and demonstrated that PRV-infection is associated with life-history, sex, catch-year and body length as a proxy for sea-age. Escaped farmed salmon (odds ratio/OR: 7.32, p<0.001) and hatchery-reared salmon (OR: 1.69 p=0.073) have higher odds of being PRV-infected than wild Atlantic salmon. Male salmon have double odds of being PRV infected compared to female salmon (OR: 2.11, p<0.001). Odds of being PRV-infected increased with body-length measured as decimetres (OR: 1.20, p=0.004). Since body length and sea-age are correlated (r=0.85 p<0.001), body length serves as a proxy for sea-age, meaning that spending more years in sea increases the odds of being PRV-infected.

Piscine myocarditis virus (PMCV) in wild Atlantic salmon Salmo salar.

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of sea-farmed Atlantic salmon Salmo salar L., but CMS-like lesions have also been found in wild Atlantic salmon. In 2010 a double-stranded RNA virus of the Totiviridae family, provisionally named piscine myocarditis virus (PMCV), was described as the causative agent of CMS. In the present paper we report the first detection of PMCV in wild Atlantic salmon. The study is based on screening of 797 wild Atlantic salmon by real-time RT-PCR. The samples were collected from 35 different rivers along the coast of Norway, and all individuals included in the study were classified as wild, based on visual appearance and scale reading. Two samples tested positive during PCR analysis, and the results were confirmed by sequencing.