Publications by authors named "Neil M Ruane"

12 Publications

  • Page 1 of 1

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7).

Dis Aquat Organ 2020 Dec 17;142:203-211. Epub 2020 Dec 17.

Fish Health Unit, Marine Institute, Oranmore H91 R673, Ireland.

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive 'piscine alphavirus'.
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http://dx.doi.org/10.3354/dao03546DOI Listing
December 2020

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.

Front Vet Sci 2020 16;7:385. Epub 2020 Jul 16.

Centre for Veterinary Epidemiology and Risk Analysis (CVERA), UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.

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.
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http://dx.doi.org/10.3389/fvets.2020.00385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7378893PMC
July 2020

Characterization of ranaviruses isolated from lumpfish L. in the North Atlantic area: proposal for a new ranavirus species (European North Atlantic Ranavirus).

J Gen Virol 2020 02 20;101(2):198-207. Epub 2019 Dec 20.

Technical University of Denmark, National Institute of Aquatic Resources, Aquatic Animal Health Unit, Kgs. Lyngby, Denmark.

The commercial production of lumpfish L. is expanding with the increased demand for their use as cleaner fish, to control sea-lice numbers, at marine Atlantic salmon L. aquaculture sites throughout Northern Europe. A new ranavirus has been isolated from lumpfish at multiple locations in the North Atlantic area. First isolated in 2014 in the Faroe Islands, the virus has subsequently been found in lumpfish from Iceland in 2015 and from Scotland and Ireland in 2016. The Icelandic lumpfish ranavirus has been characterized by immunofluorescent antibody test, optimal growth conditions and transmission electron microscopy. Partial sequences of the major capsid protein gene from 12 isolates showed 99.79-100% nt identity between the lumpfish ranaviruses. Complete genome sequencing from three of the isolates and phylogenetic analysis based on the concatenated 26 iridovirus core genes suggest these lumpfish ranavirus isolates form a distinct clade with ranaviruses from cod L. and turbot L. isolated in Denmark in 1979 and 1999, respectively. These data suggest that these viruses should be grouped together as a new ranavirus species, European North Atlantic Ranavirus, which encompasses ranaviruses isolated from marine fishes in European North Atlantic waters.
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http://dx.doi.org/10.1099/jgv.0.001377DOI Listing
February 2020

Genetic diversity among geographically distant isolates of Neoparamoeba perurans.

Dis Aquat Organ 2019 Dec;137(2):81-87

Norwegian Veterinary Institute, Pb 750 Sentrum, 0106 Oslo, Norway.

The present study explored the use of 2 common genetic markers, the mitochondrial cytochrome oxidase I (COI) and the ribosomal internal transcribed spacer (ITS) to infer the relationship between geographically distant isolates of the protozoan gill parasite Neoparamoeba perurans, the agent responsible for amoebic gill disease in farmed Atlantic salmon worldwide. Present data confirmed that the ITS marker is suitable for Neoparamoeba species discrimination; however, it is not recommended as a population marker due to the presence of multiple copies of ITS within both N. perurans clonal and polycultures. On the other hand, in the partial COI gene analysed here, a low variability was observed, with 8 haplotypes recovered from N. perurans samples collected from Europe (Ireland, Norway, Scotland) and Tasmania (Australia). In Europe, the COI haplotypes which have more recently been detected in aquaculture are different to the haplotypes associated with the original gill disease emergence in Ireland in 1997 and Norway in 2006. The presence of unique COI haplotypes in different continents suggests the presence of multiple distinct reservoirs of the pathogen in both Europe and Tasmania. Isolates from additional geographical locations are required to fully understand the origins and routes for the spread of N. perurans worldwide.
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http://dx.doi.org/10.3354/dao03433DOI Listing
December 2019

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

J Fish Dis 2019 Aug 6;42(8):1161-1168. Epub 2019 Jun 6.

Fish Health Unit, Marine Institute, Oranmore, Ireland.

Piscine myocarditis virus (PMCV) is a double-stranded RNA virus which has been linked to cardiomyopathy syndrome (CMS) in Atlantic salmon (Salmo salar L.). The first recorded outbreak of CMS in Ireland occurred in 2012. Heart tissue samples were collected in the current study from farmed Atlantic salmon from various marine sites around Ireland, and the open reading frames (ORFs) 1 and 3 were amplified and sequenced in order to examine the genetic diversity of PMCV. Results showed PMCV to be largely homogenous in Irish samples, showing little genetic diversity. However, several amino acid positions within both ORF1 and ORF3 showed consistent variations unique to the Irish PMCV strains when compared with previously published Norwegian strains. The phylogeny generated in the present study suggests that PMCV may have been introduced into Ireland in two waves, both coming from the southern part of PMCV's range in Norway. In addition, over three-quarters of the PMCV strains which were sequenced came from fish not exhibiting any clinical signs of CMS, suggesting that either PMCV is evolving to become less virulent in Ireland or Irish Atlantic salmon are developing immunity to the disease.
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http://dx.doi.org/10.1111/jfd.13018DOI Listing
August 2019

Presence and genetic variability of Piscine orthoreovirus genotype 1 (PRV-1) in wild salmonids in Northern Europe and North Atlantic Ocean.

J Fish Dis 2019 Aug 28;42(8):1107-1118. Epub 2019 May 28.

National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark.

Piscine orthoreovirus genotype 1 (PRV-1) is widespread in farmed Atlantic salmon (Salmo salar L.) populations in northern Europe, Canada and Chile. PRV-1 occurs in wild fish in Norway and Canada; however, little information of its geographical distribution in wild populations is currently available, and the effect of PRV-1 infection in wild populations is currently unknown. In this study, we present the findings of a survey conducted on 1,130 wild salmonids sampled in Denmark, Sweden, Ireland, Faroe Islands, France, Belgium and Greenland between 2008 and 2017. PRV-1 is reported for the first time in wild salmonids in Denmark, Sweden, Faroe Island and Ireland. The annual PRV-1 prevalence ranged from 0% in France, Belgium and Greenland to 43% in Faroe Islands. In total, 66 samples tested positive for PRV-1, including Atlantic salmon broodfish returning to spawn and Atlantic salmon collected at the feeding ground north of Faroe Islands. The phylogenetic analysis of S1 sequences of the PRV-1 isolates obtained in this survey did not show systematic geographical distribution. This study sheds light on the spread and genetic diversity of the virus identified in populations of free-living fish and provides rationale for screening wild broodfish used in restocking programmes.
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http://dx.doi.org/10.1111/jfd.13025DOI Listing
August 2019

Nanopore sequencing for rapid diagnostics of salmonid RNA viruses.

Sci Rep 2018 11 5;8(1):16307. Epub 2018 Nov 5.

School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, United Kingdom.

Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.
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http://dx.doi.org/10.1038/s41598-018-34464-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218516PMC
November 2018

Isolation of salmonid alphavirus subtype 6 from wild-caught ballan wrasse, Labrus bergylta (Ascanius).

J Fish Dis 2018 Nov 27;41(11):1643-1651. Epub 2018 Jul 27.

Fish Health Unit, Marine Institute, County Galway, Ireland.

The use of cleaner fish as a biological control for sea lice in Atlantic salmon aquaculture has increased in recent years. Wild-caught wrasse are commonly used as cleaner fish in Europe. In Ireland, samples of wrasse from each fishing area are screened for potential pathogens prior to their deployment into sea cages. Salmonid alphavirus was isolated from a pooled sample of ballan wrasse, showing no signs of disease, caught from the NW of Ireland. Partial sequencing of the E2 and nsP3 genes showed that it was closely related to the previously reported SAV subtype 6. This represents only the second isolation of this subtype and the first from a wild fish species, namely ballan wrasse.
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http://dx.doi.org/10.1111/jfd.12870DOI Listing
November 2018

Isolation of Streptococcus agalactiae and an aquatic birnavirus from doctor fish Garra rufa L.

Ir Vet J 2013 Sep 13;66(1):16. Epub 2013 Sep 13.

Fish Health Unit, Marine Institute, Rinville, Oranmore, Co, Galway, Ireland.

Background: The doctor fish, Garra rufa, has become increasingly popular as a treatment for skin disorders and for pedicures in recent years. Despite this there is very little information available regarding the welfare of these fish and the range of potential pathogens they may carry. In this study, a group of fish suffering from post-transport mortalities were examined and the isolated pathogens identified.

Findings: Group B Streptococcus agalactiae was isolated from kidney swabs of the fish and found to be resistant to a number of antibiotics. In addition to this, a fish virus belonging to the aquabirnavirus group, serogroup C was isolated for the first time in Ireland. However, no clinical signs of disease typical of bacterial or viral infections were observed in any fish examined.

Conclusions: As no clinical signs of disease attributable to either of the pathogens identified were found it was concluded that the mortalities were most likely due to transport related stress exacerbated by the presence of the pathogens. Further work is required to assess the suitability of current transport strategies and to examine the potential risk associated with the transport of live ornamental fish.
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http://dx.doi.org/10.1186/2046-0481-66-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847237PMC
September 2013

Critical role of the matricellular protein SPARC in mediating erythroid progenitor cell development in zebrafish.

Cells Tissues Organs 2013 24;197(3):196-208. Epub 2012 Nov 24.

Aquatic Molecular Pathobiology Laboratory, Instituto Investigaciones Marinas, Consejo Superior de Investigaciones Científicas, Vigo, Spain.

Sparc (osteonectin) is a multifunctional matricellular glycoprotein expressed by many differentiated cells. Members of this family mediate cell-matrix interactions rather than acting as structural components of the extracellular matrix (ECM); therefore, they can influence many remodelling events, including haematopoiesis. We have investigated the role of sparc in embryonic haematopoiesis using a morpholino antisense oligonucleotide-based knockdown approach. Knockdown of sparc function resulted in specific erythroid progenitor cell differentiation defects that were highlighted by changes in gene expression and morphology, which could be rescued by injection of sparc mRNA. Furthermore, a comparison of blood phenotypes of sparc and fgfs knockdowns with similar defects and the sparc rescue of the fgf21 blood phenotype places sparc downstream of fgf21 in the genetic network regulating haematopoiesis in zebrafish. These results establish a role for an ECM protein (Sparc) as an important regulator of embryonic haematopoiesis during early development in zebrafish.
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http://dx.doi.org/10.1159/000343291DOI Listing
September 2013

Gill damage to Atlantic salmon (Salmo salar) caused by the common jellyfish (Aurelia aurita) under experimental challenge.

PLoS One 2011 Apr 7;6(4):e18529. Epub 2011 Apr 7.

Coastal and Marine Research Centre, Environmental Research Institute, University College Cork, Cork, Ireland.

Background: Over recent decades jellyfish have caused fish kill events and recurrent gill problems in marine-farmed salmonids. Common jellyfish (Aurelia spp.) are among the most cosmopolitan jellyfish species in the oceans, with populations increasing in many coastal areas. The negative interaction between jellyfish and fish in aquaculture remains a poorly studied area of science. Thus, a recent fish mortality event in Ireland, involving Aurelia aurita, spurred an investigation into the effects of this jellyfish on marine-farmed salmon.

Methodology/principal Findings: To address the in vivo impact of the common jellyfish (A. aurita) on salmonids, we exposed Atlantic salmon (Salmo salar) smolts to macerated A. aurita for 10 hrs under experimental challenge. Gill tissues of control and experimental treatment groups were scored with a system that rated the damage between 0 and 21 using a range of primary and secondary parameters. Our results revealed that A. aurita rapidly and extensively damaged the gills of S. salar, with the pathogenesis of the disorder progressing even after the jellyfish were removed. After only 2 hrs of exposure, significant multi-focal damage to gill tissues was apparent. The nature and extent of the damage increased up to 48 hrs from the start of the challenge. Although the gills remained extensively damaged at 3 wks from the start of the challenge trial, shortening of the gill lamellae and organisation of the cells indicated an attempt to repair the damage suffered.

Conclusions: Our findings clearly demonstrate that A. aurita can cause severe gill problems in marine-farmed fish. With aquaculture predicted to expand worldwide and evidence suggesting that jellyfish populations are increasing in some areas, this threat to aquaculture is of rising concern as significant losses due to jellyfish could be expected to increase in the future.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018529PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072396PMC
April 2011

Intra-adrenal interactions in fish: catecholamine stimulated cortisol release in sea bass (Dicentrarchus labrax L.).

Comp Biochem Physiol A Mol Integr Physiol 2006 Mar 27;143(3):375-81. Epub 2006 Jan 27.

Centre for Marine Sciences (CCMAR), Campus de Gambelas, University of Algarve, 8005-139 Faro, Portugal.

The effect of the catecholamines, adrenaline and noradrenaline, on sea bass (Dicentrarchus labrax) and sea bream (Sparus auratus) interrenal cortisol production was studied in vitro using a dynamic superfusion system technique. Increasing concentrations of catecholamines (10(-6), 10(-8) and 10(-10) M) stimulated cortisol production in a dose-dependent manner, in sea bass only. The increase in cortisol production stimulated by adrenaline (10(-6) M) and noradrenaline (10(-6) M) was inhibited by sotalol (2 x 10(-5) M), but not by prazosin suggesting that catecholamines stimulate cortisol release through the beta-receptor subtype. To evaluate catecholamine-induced signal transduction in head kidney cells, measurements of cAMP production and [H3]myo-inositol incorporation were determined in head kidney cell suspensions. Adrenaline and noradrenaline (10(-6) M) increased cAMP production, but had no effect on total inositol phosphate accumulation. These results indicate that catecholamines released from the chromaffin cells within the interrenal tissue may act as a paracrine factor to stimulate interrenal steroidogenesis in the sea bass.
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http://dx.doi.org/10.1016/j.cbpa.2005.12.027DOI Listing
March 2006