October 2021
Professor Simon More re-elected Chair of EFSA's Scientific Committee
Professor Simon More was recently re-elected Chair of the Scientific Committee (SC) of the European Food Safety Authority (EFSA) for a second three-year team, from 2021-2024. The SC is EFSA’s overarching scientific panel, bringing together the Chairs of each of EFSA’s ten Scientific Panels (focusing on different areas of the food and feed chain) plus six independent experts. The SC supports the work of the panels on cross-cutting issues, and focuses on the development of harmonised risk assessment methodologies in fields where EU-wide approaches are not yet defined.
An evaluation of four private animal health and welfare standards and associated quality assurance programmes for dairy cow production
Private standards in animal health and welfare (AHW) and associated quality assurance (QA) programmes have the potential to substantially improve AHW. However, there are concerns that they do not necessarily do so. In this study, we evaluated four private AHW standards and associated QA programmes for dairy cow production, from Denmark, Ireland, the Netherlands and the UK, using an existing (but adapted) conceptual framework. We found limited objective information to support programme claims, although there were considerable differences between programmes. Across all programmes, problems were identified with respect to transparency, and attempts to scrutinise claims would not be a straightforward process for most consumers. Among the programmes, there were notable examples of best-practice in AHW. There is a strong case for regulatory oversight of private standards in AHW and associated QA programmes. [(opens in a new window)More et al. Food Policy (in press) available shortly].
Spatio-temporal models of bovine tuberculosis in the Irish cattle population, 2012-2019
In Ireland, the incidence rate for bovine tuberculosis (bTB) varies by herd and location. It is hoped that statistical disease-mapping models accounting for both spatio-temporal correlation and covariates might contribute towards explaining this variation. This study, conducted by Madden et al. in collaboration with the University of Limerick and the Department of Agriculture, Food and the Marine, highlights national bTB incidence rates and suggests that shifting from national level analysis to smaller geographical regions may help identify localised high-risk areas. [(opens in a new window)Madden et al. Spatial and Spatio-temporal Epidemiology 39, 100441].
Protective immunity against tuberculosis in a free-living badger population vaccinated orally with Mycobacterium bovis Bacille Calmette Guérin (BCG)
In experimental trials, vaccination of badgers with Mycobacterium bovis Bacille Calmette–Guérin (BCG) has been shown to protect badgers against tuberculosis. This is supported by results from the 3-year County Kilkenny BCG vaccine field study, which suggest that BCG vaccination of badgers could be a highly effective means of reducing the incidence of tuberculosis in badger populations. The results are consistent with an indirect protective effect in the non-vaccinated badgers leading to a high level of population immunity. This study was led by the UCD Tuberculosis Diagnostics and Immunology Research Laboratory with colleagues from CVERA and the Department of Agriculture, Food and the Marine. [(opens in a new window)Gormley et al. Transboundary and Emerging Diseases (in press)].
Pre-symptomatic transmission of SARS-CoV-2 infection: a secondary analysis using published data
Using published data, this study estimated the proportion of pre-symptomatic transmission of SARS-CoV-2 infection that can occur, and the timing of transmission relative to symptom onset. The estimated mean transmission time relative to symptom onset ranged from −2.6 (95% CI −3.0 to –2.1) days before infector symptom onset to 1.4 (95% CI 1.0 to 1.8) days after symptom onset, and the proportion of pre-symptomatic transmission ranged from 45.9% (95% CI 42.9% to 49.0%) to 69.1% (95% CI 66.2% to 71.9%). There is substantial potential for pre-symptomatic transmission of SARS-CoV-2 across a range of different contexts, highlighting the need for rapid case detection, contact tracing and quarantine. The study was led by Miriam Casey-Bryars in collaboration with the staff from the DAFM One Health Scientific Support Unit, the Health Information and Quality Authority, the UCD School of Veterinary Medicine and other UCD research centres. [(opens in a new window)Casey-Bryars et al. BMJ Open 11, e041240].
Population mobility trends, deprivation index and the spatio-temporal spread of Coronavirus disease 2019 in Ireland
Like most countries worldwide, the coronavirus disease (COVID-19) has adversely affected Ireland. This study investigated the spatio-temporal trend of COVID-19 incidence; described mobility trends as measured by aggregated mobile phone records; and investigated the association between deprivation index, population density and COVID-19 cases while accounting for spatial and temporal correlation. Despite adjustment for population density and the average number of persons per room, Madden et al found an association between deprivation index and COVID-19 incidence for the most deprived quintile compared to the least deprived. There was a large range of spatial heterogeneity in COVID-19 cases in Ireland. The results suggest that prioritising densely populated deprived areas (that are at increased risk of comorbidities) during vaccination rollout may capture people that are at risk of infection and, potentially, also those at increased risk of hospitalisation. The study was conducted in collaboration with the Health Information and Quality Authority, the National University of Ireland Maynooth and the University of Limerick. [(opens in a new window)Madden et al. International Journal of Environmental Research and Public Health 18, 6285].
Trends in estimated intramammary antimicrobial usage in the Irish dairy industry from 2003 to 2019
Understanding antimicrobial (AM) usage is key to safely reducing the use of antimicrobials in food-producing animals and as part of addressing the global public health threat of AM resistance. The authors estimated intramammary AM usage in Ireland from national sales data for the period 2003 to 2019, updating previous work. Use of blanket dry cow therapy is still widespread. In addition, there was evidence of ongoing use of highest priority & critically important AMs. This study provides objective evidence in support of efforts to direct and prioritize urgent changes in AM prescribing and usage as well as securing farm-level and prescriber-level data in Ireland. This study was led by Catherine McAloon from the UCD School of Veterinary Medicine in association with CVERA and Animal Health Ireland. [(opens in a new window)McAloon et al. JDS Communications 2, 271-276].
The Irish Johne’s control programme
This study by Gavey et al. presents detail of the Irish Johne's Control Programme (IJCP), which provides a long-term approach to the voluntary control of Johne's disease (JD) in Ireland, strongly supported by Irish cattle industry leadership. It leverages the establishment of Animal Health Ireland for control of animal diseases not regulated by the European Union. The programme objectives including facilitating protection against spread of JD to uninfected farms, reducing the level of infection when present, assuring markets of JD control in Ireland, and improving calf health and farm biosecurity. The programme will continue to innovate and improve to meet farmer and industry needs. [(opens in a new window)Gavey et al. Frontiers in Veterinary Science 8, 703843].
The Irish programme to eradicate bovine viral diarrhoea virus – organization, challenges and progress
This paper presents a detailed overview relevant to the organisation, challenges and progress in the Irish programme to eradicate bovine viral diarrhoea (BVD) from Ireland. The mandatory national eradication programme, coordinated by Animal Health Ireland, commenced in 2013. A key challenge in the early years, highlighted by modeling, was the retention of PI animals by some herd owners. This has largely been resolved by measures including graduated financial supports to encourage their early removal, herd-level movement restrictions, ongoing programme communications and the input of private veterinary practitioners (PVPs). The prevalence of PI calves in 2013 was 0.66%, within 11.3% of herds, reducing in each subsequent year, to 0.03 and 0.55%, respectively, at the end of 2020. Recent regulatory changes within the European Union for the first time make provision for official approval of national eradication programmes, or recognition of BVD freedom, and planning is underway to seek approval and, in due course, recognition of freedom within this framework by 2023. The study was led by Dr. David Graham, CEO of Animal Health Ireland in collaboration with UCD CVERA, the Irish Cattle Breeding Federation, DAFM, the Helmholtz Centre for Environmental Research GmbH - UFZ in Germany and Animal Health and Welfare NI. [(opens in a new window)Graham et al. Frontiers in Veterinary Science 8, 674557].
Dr Áine Collins
Recently, Dr Áine Collins moved to a new role as Expert in Food and Waterborne Diseases and Legionnaire’s Disease in the Emerging, Food and Vector-Borne Diseases Programme in the European Centre for Disease Prevention and Control in Stockholm, Sweden. During her time in CVERA, Áine contributed to several study areas including COVID-19, Schmallenberg virus, antimicrobial usage, cattle movements, bovine tuberculosis and the national pig population. Though her time in CVERA was brief, Áine will be greatly missed, both professionally and personally, and we wish her well in her new role.
May 2021
Stewardship of intramammary antimicrobials
The Veterinary Medicines Regulation (2019/6) will apply in Ireland from 22 January 2022, with an emphasis on prudent and responsible antimicrobial usage. Relevant to this Regulation, the Veterinary Council of Ireland (VCI) approached the CellCheck technical working group (TWG) for technical perspectives on key definitions and prescribing guidelines for dry-cow and intramammary antimicrobials. The TWG, chaired by Simon More, includes a group of 18 technical experts drawn from all relevant fields and a broad range of organisations. In its submission to the VCI, the TWG focused on prescribing guidelines for veterinarians, animal- and herd-level information to inform prudent prescribing, and accompanying national actions to address suboptimal mastitis and support prudent prescribing. The TWG submission has been presented at several public fora, including the Oireachtas Joint Committee for Agriculture and the Marine (on 23 March), a meeting of iNAP (Ireland’s National Action Plan on Antimicrobial Resistance; on 29 March) and the CellCheck Implementation Group (on 07 April).
Future risk of bovine tuberculosis (Mycobacterium bovis) breakdown in cattle herds 2013-2018: a dominance analysis approach
A paper on the future risk of bovine tuberculosis, led by Byrne et al from the DAFM One Health Scientific Support Unit, has been published. In this study, the future risk of herd breakdowns (BD) were estimated, for the cohort of herds that were derestricted during 2013 in Ireland using multivariable logit regression models, with a dominance analysis approach. BD length was a significant predictor of future risk, primarily driven by long BDs > 230 days relative to short BDs < 130 days (OR 95%CI: 1.157–1.851), as was having had a previous BD (OR 95%CI: 1.012–1.366). Herd-size was the dominant predictor of future risk (accounted for 46% of predicted variance), suggesting significant increase in risk of future breakdown with increasing (log) herd-size (OR 95%CI: 1.378–1.609). There was significant spatial variation in future risk across counties, and it was the second most dominant predictor of future risk (25% of predicted variance). In contrast, the size of index breakdowns was not a strong predictor of future risk over a 5-year period. [(opens in a new window)Byrne et al. Microorganisms 9, 1004].
Epidemiological parameters for COVID-19 modelling
Since the start of the pandemic, CVERA have contributed to national efforts in epidemiological COVID-19 modelling (IEMAG; the Irish Epidemiological Modelling Advisory Group to NPHET). As part of this work, there has been a need for a detailed understanding of a range of epidemiological parameters based on all available published information. Previously, CVERA contributed to published papers on the serial interval and generation time, the incubation period, and the duration of the infectious period of COVID-19. Recently, there have been further publications, on the relative infectiousness of symptomatic and asymptomatic individuals [(opens in a new window)McElroy et al. BMJ Open 11, e042354], on pre-symptomatic transmission of SARS-CoV-2 infection [Casey-Bryars et al. BMJ Open (in press)], and on serial interval and the proportion of transmission events that can be attributed to pre-symptomatic transmission, based on contact tracing data from Ireland [(opens in a new window)McAloon et al. BMC Public Health 21, 805]. In addition, CVERA has produced weekly outputs to IEMAG through the analysis of anonymised mobile phone records and high-resolution geocoded case data, to monitor population movement and the spatial spread of the disease. In addition, a spatio-temporal model has been developed to explore the association between deprivation index and COVID-19 incidence [Madden et al. submitted]. Results suggest that prioritising densely populated, deprived areas (that are at increased risk of comorbidities) during vaccination rollout may capture people that are at risk of infection and, potentially, also those at increased risk of hospitalisation.
A systematic framework of modelling epidemics on temporal networks
A paper by Humphries et al the UCC School of Mathematical Sciences presents a modelling framework for the spread of epidemics on temporal networks. The proposed temporal pair-based model that is systematically derived from this framework offers an improvement over existing pair-based models by moving away from edge-centric descriptions while keeping the description concise and relatively simple. We show that the shift in perspective from individual-based to pair-based quantities enables exact modelling of Markovian epidemic processes on temporal tree networks. On arbitrary networks, the proposed pair-based model provides a substantial increase in accuracy at a low computational and conceptual cost compared to the individual-based model. From the pair-based model, we analytically find the condition necessary for an epidemic to occur, otherwise known as the epidemic threshold. [(opens in a new window)Humphries et al. Applied Network Science 6, 23].
A large-scale epidemiological model of BoHV-1 spread in the Irish cattle population to support decision-making in conformity with the European Animal Health Law
Infectious bovine rhinotracheitis (IBR), caused by the virus BoHV-1, is currently endemic in Ireland. This is in contrast to many countries in continental Europe where there has been a rapid move towards BoHV-1 freedom. Building on earlier work in support of the bovine viral diarrhoea (BVD) eradication programme, Jonas Brock of Animal Health Ireland (AHI) has developed a large-scale epidemiological model of BoHV-1 in the Irish cattle population, which has offered the opportunity to evaluate a range of eradication options for Ireland, both in terms of effectiveness and cost-effectiveness, whilst ensuring compliance with key principles as outlined in the EU Animal Health Law. This work is being undertaken in collaboration with colleagues from the Helmholtz Centre for Environmental Research GmbH - UFZ in Leipzig (Germany), AHI and CVERA. As part of his work, Jonas has made some important methodological advances. In particular, animal movement is now an emergent property of this model, which allows BoHV-1 control scenarios to be modelled into the future, beyond the period when animal movement data are available. [(opens in a new window)Brock et al. Preventive Veterinary Medicine 192, 105375].
Epidemiological drivers of Bovine Viral Diarrhoea Virus once herd prevalence is low
An eradication programme for bovine viral diarrhoea (BVD) has been in place since 2013, leading to a year-on-year reduction in BVD herd incidence. This study was undertaken to understand the risk of herd infection towards the latter stages of eradication, when herd prevalence is low. In particular, we were interested in the drivers of BVD infection in those herds that were positive for the first time in 2019. A generalised linear mixed model, including a county level random effect, was used to investigate the impact of herd size, management system, measures of proximity to infected herds, and measurements of inward movement. The best-fit model explaining the probability of being a case retained herd size, a network measurement of spatial proximity to BVD infected herds and potential Trojan dams (pregnant animals brought into the herd that could potentially be carrying infected calves in utero). These findings may help target both the end-stages of Ireland’s BVD eradication programme and post-eradication surveillance. Miriam Casey, Jamie Tratalos and Simon More of CVERA collaborated with colleagues from Animal Health Ireland and the Department of Agriculture, Food and the Marine to deliver this project which is currently being prepared for submission to a peer-reviewed journal.
EuFMDiS national foot-and-mouth disease transmission model for Ireland
CVERA worked with the National Disease Control Centre (NDCC) of the Department of Agriculture, Food and the Marine (DAFM) and with the European Commission for the Control of Foot and Mouth Disease (EuFMD) to parameterise the (opens in a new window)EuFMDiS model for Ireland. This model can be used to evaluate various control options to eradicate the foot-and-mouth disease (FMD). It can also evaluate available resource and vaccine supply issues. CVERA collated cattle, pig, sheep and goat population, movement and management system data from Ireland and provided measures of indirect contacts. We collaborated with EuFMDiS modellers and DAFM stakeholders to parameterise a national FMD transmission model for Ireland. The Irish model is used by the NDCC as part of a Europe wide project using FMD transmission simulations to explore various control options and resource usage. A project entitled “(opens in a new window)Impact of on-farm biosecurity level in pig herds on the spread and control of foot-and-mouth disease,” based upon the Irish FMD model was recently presented by EuFMD collaborators at the Open Session of EuFMD.
Livestock disease resilience: from individual to herd level
In the context of animal disease control, vaccination and animal breeding each has the potential to protect the individual, allowing animals to maintain performance in the face of a pathogen challenge. These can be considered ‘direct vaccine effects’ in veterinary epidemiology, and ‘individual disease resilience’ in animal breeding. Vaccination and animal breeding also have the potential to protect the herd through ‘indirect effects’ that impact on the pathogen load in the environment (by reducing susceptibility to infection, reducing the magnitude of infectiousness, and reducing the duration of the infectious period). In animal breeding, this is known as ‘herd disease resilience’. As a collaboration between the Roslin Institute in Scotland, Genus-PIC in Germany and CVERA, this paper highlights the shared goals of animal breeding and veterinary epidemiology in animal disease control and seeks to clarify differences in terminology to facilitate further collaborative approaches to sustainable control of infectious diseases in livestock. [(opens in a new window)Doeschl-Wilson et al. Animal (in press)] will be available shortly.
Protecting bees: a new way forward for risk assessment
A new scientific opinion from the European Food Safety Authority has just been published, to coincide with World Bee Day (20 May), setting out an integrated, holistic framework to assess the combined effects of multiple stressors on honey bees. This work was requested by the European Parliament's Committee for the Environment, Public Health and Food Safety (ENVI), and is a major step forward in efforts to help reverse the decline of insect pollinators in Europe by proposing a new approach to the environmental risk assessment of honey bees. Simon More chaired the working group that developed this opinion. For more information, please visit (opens in a new window)here.
Key learnings during the development of a generic data collection tool to support assessment of freedom of infection in cattle herds
Many EU Member States have implemented control or eradication programmes for endemic infectious diseases in cattle. However, the design of these programmes varies between countries and comparison is complex. Although output-based methods (to estimate the confidence of freedom) are under development, there is as yet no practical framework that could be applied to a variety of infectious diseases. A data collection tool to address this issue was developed by experts from two international projects, including STOC free (Surveillance Tool for Outcome-based Comparison of FREEdom from infection, (opens in a new window)www.stocfree.eu) and SOUND control (Standardizing OUtput-based surveillance to control Non-regulated Diseases of cattle in the EU, (opens in a new window)www.sound-control.eu). This paper outlines the lessons that were learned during the development of this data collection tool, which was used both for the evaluation of data availability and during actual data collection. These lessons will assist with the development of any generic data collection tool for animal disease control purposes, and will also facilitate development of output-based modelling frameworks that aim to calculate confidence of freedom from infection. [(opens in a new window)van Roon et al. Frontiers in Veterinary Science 8, 656336].
February 2021
Ongoing projects
A wide range of projects are ongoing in CVERA at any one time. Some projects are led or co-ordinated by CVERA members while others, led by members of other departments or organisations, require specific support or analysis. Some of the projects that CVERA members are currently leading include i) the development of a quantitative risk assessment methodology for cheese made from unpasteurised milk from cows subsequently identified as being infected with Mycobacterium bovis, ii) the quantification of local bovine tuberculosis (bTB) transmission in badgers and cattle with and without vaccination of badgers (Meles meles) in Ireland, iii) the spatial structure of farms in Ireland, iv) spatio-temporal models of bovine tuberculosis in the Irish cattle population, 2012-2019, iv) an analysis of the role of cattle movements in the transmission of bovine tuberculosis, and v) risk factors for recent Bovine Viral Diarrhoea (BVD) outbreaks on farms with long-term history of freedom. The studies mentioned above are a small example of the projects to which CVERA members are currently contributing to. Several of these projects are nearing completion and all will help to inform policy in the future.
Combining expert knowledge and machine-learning to classify herd types in livestock systems
A paper by Jonas Brock and Colleagues from the Department of Ecological Modelling at the Helmholtz Centre for Environmental Research GmbH-UFZ in Germany, Animal Health Ireland and UCD CVERA recently published a paper on "Combining expert knowledge and machine-learning to classify herd types in livestock systems" in Scientific Reports. The study presents a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs The authors provide a data-driven classification tree using decisions derived from the Irish livestock registration data. In total, 17 different herd types were identified in Ireland, including four different dairy herd types: typical dairy herds (male calves sold within a few weeks of birth, most female calves reared as replacements), dairy farms that rear both female and male calves, dairy herds that use contract rearing for their heifer calves, and dairy farms that rely on purchase of replacement heifers and cows. This approach will be applicable across a broad range of epidemiological studies in Ireland, providing a method to accurately classify herds with a high level of resolution. To the authors’ knowledge, this is the first time that the SOM algorithm has been used to differentiate livestock systems. The paper is available at (opens in a new window)Scientific Reports 11, 2989.
Development and application of a prioritisation tool for animal health surveillance activities in Ireland
Anne Marie Clarke from the One Health One Welfare Scientific Support Unit in the Department of Agriculture, Food and the Marine has published a paper on the “Development and application of a prioritisation tool for animal health surveillance activities in Ireland” in Frontiers in Veterinary Science. Decisions around animal health management by stakeholders are often subject to resource limitation, and prioritisation is needed to evaluate whether effort is attributed appropriately. In this paper, the authors describe the development and implementation of such a prioritization tool. In this study, antimicrobial resistance and bovine tuberculosis were ranked top of the endemic diseases/conditions in the Irish context, while African swine fever and foot and mouth disease were ranked top of the exotic diseases/conditions by the stakeholders. The paper is available at (opens in a new window)Frontiers in Veterinary Science 7, 596867.
Modelling transmission and control of Mycobacterium avium subspecies paratuberculosis within Irish dairy herds with compact spring calving
Modelling studies are increasingly used in support of national animal disease control/eradication programmes, to evaluate the impact of different policy options on programme progress into the future. Floor Biemans with colleagues from INRAE in France, Teagasc and UCD CVERA in Ireland have published a paper on “Modelling transmission and control of Mycobacterium avium subspecies paratuberculosis within Irish dairy herds with compact spring calving” in Preventive Veterinary Medicine. In this work, Floor has adapted an existing French model to Irish conditions, to better understand Map transmission in Irish dairy herds. The current paper describes this adaptation process, specifically relating to within-herd events. The paper is available at (opens in a new window)Preventive Veterinary Medicine 186, 105228.
Stakeholder perceptions of non-regulatory bovine health issues in Ireland: past and future perspectives
A paper by Natascha Meunier and colleagues from Animal Health Ireland, UCD CVERA and the Department of Management, School of Business & Humanities, TU Dublin recently published a paper on “Stakeholder perceptions of non-regulatory bovine health issues in Ireland: past and future perspectives” in the Irish Veterinary Journal. There have been multiple (political, environmental, cultural) drivers of change in Irish agriculture in recent years, including the establishment of Animal Health Ireland (AHI) in 2009. In this study, the authors describe the opinion of stakeholders (farmers, veterinary practitioners and agricultural industry professional service providers) on their perceptions of changes in selected non-regulatory bovine health issues over the last 10 years and priority issues relevant to non-regulatory bovine health to be tackled over the next 10 years. Three priorities relevant to non-regulatory bovine animal health over the next 10 years were identified, including antimicrobial resistance (highlighting measures to reduce both on-farm usage and resistance), anthelmintic resistance, greenhouse emissions and calf welfare, which aligns closely with broader societal concerns. This information is useful to AHI, particularly with respect to future priorities. The paper is available at (opens in a new window)Irish Veterinary Journal 73, 25.
Recent presentations
During January 2021, Simon More presented on three diverse topics relevant to CVERA, including:
- ‘Veterinary contributions to the national COVID-19 response’, at the annual CAVI conference
- ‘Bridging the gap between epidemiology and quantitative genetics: bovine tuberculosis as a case study’ at an international conference in honour of Professor John Woolliams, who has retired from the Roslin Institute, Scotland
- ‘Towards an integrated and holistic risk assessment of multiple stressors in honey bees’, to the Environment, Public Health and Food Committee of the European Parliament
The latter presentation coincided with the launch of the draft scientific opinion on a systems-based approach to the environmental risk assessment of multiple stressors in honey bees by the Scientific Committee of the European Food Safety Authority. Further detail is available at (opens in a new window)here.
The Seventh International Conference on Mycobacterium bovis (M. bovis 2022)
After postponing the original conference last March, the M. bovis Committee reconvened recently to discuss options. The Committee agreed that it is not feasible to hold the conference in 2021, as many people are reluctant to, or restricted from, international travel. We also decided against holding a virtual event as we believe that one of the major strengths of the M. bovis conference is that it allows our small international community of researchers, decision makers and industry members to meet, network and socialise together in person. Taking these issues into account and subject to future pandemic guidelines, we have decided to host the M. bovis conference in June 2022 in Galway, Ireland. Please visit (opens in a new window)https://www.mbovis2022.com/ or follow the conference (opens in a new window)@mbovis2022 for more information.