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Lead partner: Marine Institute, Oranmore, Co. Galway. Project Partners: Vet Aqua International, Oranmore, Co. Galway., Global Trust Certification Ltd., Dundalk, Co. Louth. Project duration: 01/10/2008 to 31/10/2011, The AquaPlan project brought together key stakeholders from the finfish aquaculture industry and state agencies with the aim of drafting and implementing a national strategic plan for fish health in Ireland. Many countries already have well established comprehensive strategies for managing aquatic animal health which are deemed necessary for the sustainable development of the industry. A range of deliverables were produced by the project which are all essential components of the strategic plan for fish health management., Funder: Ireland's EU structural funds programme 2007-2013, co-funded by the Irish government and the European Union- European Regional Development Fund, Marine Institute. Grant-Aid agreement no. PBA/AF/08/003(01)

Genetics of disease Microarrays Variant genotypes Population genetics Sequence alignment Alleles The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians. Whole genome sequencing to discover genetic variants underlying type-2 diabetes, coronary heart disease and related phenotypes amongst Indian Asians. Imperial College Healthcare NHS Trust cBRC 2011-13 (JS Kooner [PI], JC Chambers).

Peer-reviewed.Released with a Creative Commons Attribution Non-Commercial No Derivatives License, Observed emergence of IPNV in farmed Irish salmon is simulated using a model originally developed to analyse the spread of the virus in Scotland [Murray, A.G., 2006a. A model of the spread of infectious pancreatic necrosis virus in Scottish salmon farms 1996–2003. Ecol. Model. 199, 64–72]. IPNV appears to have become established relatively recently in Ireland and the model is altered to explicitly simulate the origin of the spread of the virus. Input to freshwater farms was key to initiation of infection, but modelling suggests that endogenous spread was responsible for much of the subsequent increase in prevalence of IPNV. From the modelling, it is unlikely that direct imports accounted for most IPNV cases. If this is the case, cessation of imports, without a substantial improvement in biosecurity, would be likely to be of only limited effect in controlling IPNV. Marine IPNV prevalence appears to be insensitive to direct interventions in the marine environment (as in the Scottish model). A multi-element control strategy, targeting both endogenous spread and external input of infection and prioritising freshwater sites, but extending to marine sites, would probably now be required to eradicate IPNV from Ireland.

Infectious pancreatic necrosis (IPN) is an economically significant viral disease of salmonid fish worldwide. Infectious pancreatic necrosis is categorised as a List III disease under Annex A of EU Council Directive 91/67/EEC. List III diseases are present within the EU and up to 2004 were regulated under national control programmes within each member state. The disease was first described in freshwater trout in North America in the 1950’s (Wood et al., 1955) and has been reported in Europe since the early 1970’s (Ball et al., 1971). Initially, IPN was regarded as a serious disease affecting rainbow trout fry and fingerlings (Roberts & Pearson, 2005). However as the salmon farming industry began to expand during the 1970’s, incidence of IPN disease in salmon also increased with the result that IPN is now widespread in the salmon farming industry in both Norway and Scotland. The economic loss due to the disease is large and outbreaks may occur in Atlantic salmon juveniles in fresh-water and in post-smolts after transfer to sea-water. Historically in Ireland, isolations of the IPN virus have been rare and occasional outbreaks have occurred in both rainbow trout and Atlantic salmon facilities. The Marine Institute and its predecessor, the Fisheries Research Centre, have been testing farmed and wild fish for disease pathogens since the mid 1980’s. The first reported clinical outbreak of IPN in Atlantic salmon occurred in 2003. However in 2006 severe outbreaks in a number of freshwater salmon hatcheries occurred which were all linked to imports from a specific single source. To date, clinical outbreaks of IPN in Ireland have been associated with imports of infected ova and their subsequent movement within the country. This report reviews the prevalence of the IPN virus in the Irish salmon farming industry and also in wild fish from selected rivers. It describes the steps taken by the industry to control the disease in 2006 and aims to provide some practical solutions to reduce the prevalence of the virus in farmed and wild fish and to prevent future outbreaks of the disease., Funder: Marine Institute

Pancreas Disease is the most significant single infectious disease affecting marine salmon farms in Ireland. The first epidemiological studies of Pancreas Disease (PD) in Ireland in the early 1990’s indicated that significant losses occurred in farmed Atlantic salmon in their first year at sea on some individual farms (Menzies et al., 1996). A serological survey for the presence of Salmon Pancreas Disease Virus (SPDV) antibody in 1996 revealed that 53% of Irish sites were positive, but that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998) and this pattern persisted throughout the remainder of the 1990’s. In 2002, a serious increase in both the incidence and severity of PD was reported on farmed Atlantic salmon marine sites in Ireland. An epidemiological survey of Irish sites for 2002 revealed that 59% of sites reported an outbreak of PD, with mortalities averaging 12% (range 1 – 42%; McLoughlin et al., 2003). A recent study using data collected for 2003 and 2004 indicated that PD occurred in 62% and 86% of sites respectively. The average mortality due to PD on affected farms was 18.8% in 2003 and 14.8% in 2004. In response to these significant losses due to PD a range of research initiatives was launched in Ireland and was supported by the Marine Institute. This document gives an overview of the most recent findings from the current projects, carried out in 2004/2005 and also provides an overview of the various actions in Scotland and Norway, where PD has also become a disease of economic significance in salmon aquaculture., Funder: Marine Institute

This report details the investigations into a major mortality of farmed salmon at Inver Bay and McSwyne’s Bay, Co. Donegal in July 2003. Previous reports were provided on 29th July 2003 and on 11th August 2003. The information is based upon analysis and research by MI scientists, a review of environmental data, survey reports by external consultants, inputs from veterinary practitioners who visited the site, reports from DCMNR staff in Killybegs, and site visits made by DCMNR / MI inspectors. Following a review meeting of the principal investigators on the 9th October, 2003, MI proceeded to carry out further scientific investigations. DCMNR also commissioned Kirk McClure Morton Consulting Engineers (KMM) to carry out a parallel investigation of the mortalities at Inver Bay and McSwynes Bay salmon farms. MI provided support as required to the KMM study, the report for which was furnished to DCMNR and MI on 11 February 2004. (KMM, 2004) MI wishes to acknowledge the high level of co-operation and assistance that it received from the owners and staff of Creevin Fish Farm Ltd, Eany Fish Products Ltd and Ocean Farms Ltd. It also wishes to acknowledge the assistance of veterinary practitioners, DCMNR staff and others in the course of this investigation., Funder: Marine Institute

In the early 1990’s pancreas disease (PD) was shown to be the most significant cause of mortality in Irish farmed salmon (Wheatley et al., 1995, Menzies et al., 1996, Crockford et al., 1999). At that time the aetiology of PD was uncertain but in 1995 it was conclusively shown that PD was caused by a virus subsequently named salmon pancreas disease virus (SPDV), (Nelson et al., 1995, McLoughlin et al., 1996). It has since been further classified and named salmonid alphavirus (Weston et al., 1999, Weston et al., 2002). The clinical and histopathological features of naturally occurring pancreas disease in farmed Atlantic salmon in Ireland were described by Murphy et al., 1992 and McLoughlin et al., 2002. The original epidemiological studies of PD in Ireland indicated that mortality rates up to 48% have occurred in farmed Atlantic salmon in their first year in the sea on some individual fish farms (Menzies et al., 1996). PD was recorded in over 70% of marine sites monitored and the majority of PD outbreaks occurred during August to October (Crockford et al., 1999). A serological survey for the presence of SPDV antibody in 1996 revealed 53% of the sites (9/17) were positive and that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998). This pattern persisted until 2002 when there was a serious increase in both the incidence and severity of PD reported on farmed Atlantic salmon marine sites in Ireland. In order to identify factors associated with this re-emergence of PD in Irish farmed salmon, an in-depth epidemiological investigation was carried out on all marine sites. In trying to identify the cause of a disease from epidemiological studies the concept of time, place and individual is paramount, i.e. why did a particular disease occur in a particular animal or group of animals at a particular time in a particular place? Epidemiological study designs are chosen so that predictor variables are measured in affected and non-affected “units”. These “units” may be cells, animals, pens, farms or countries. The association between these predictor variables and disease is then examined. Where associations are demonstrated then risk factors for disease can be identified. A risk factor is a predictor variable associated with the disease. However the identification of a risk factor does not imply causation. The strength, consistency, temporality and dose response effect of the risk factor add weight to it being causal but only an intervention study where the risk factor is added or omitted can confirm this. Individual or univariate analysis of the relationship between a predictor variable and disease may result in an association being demonstrated. However it is dangerous to read too much into univariate analyses as factors which have been ignored, not measured or not seen as important may have a confounding effect. Multivariate analysis is used to try to provide estimates of association adjusted for the effect of confounding factors is a much more accurate and powerful epidemiological tool, but was of limited application in this snapshot survey of a single production cycle. This report aims to describe the occurrence and severity of PD in Irish farmed salmon in 2002-2003 and to identify risk factors associated with the re-emergence of severe PD. Finally, recommendations are made on how PD can be managed to reduce its serious impact on the health, welfare and productivity of Irish farmed salmon., Funder: Marine Institute

Peer-reviewed, This report described the first detections of koi herpesvirus (KHV) in the Republic of Ireland in imported koi carp. In both cases the KHV suspicions were confirmed by molecular diagnosis and the infected stocks culled., Funder: Marine Institute