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The Scientific Committee (SC) reconfirms that the benchmark dose (BMD) approach is a scientifically more advanced method compared to the no-observed-adverse-effect-level (NOAEL) approach for deriving a Reference Point (RP). The major change compared to the previous Guidance (EFSA SC, 2017) concerns the Section 2.5, in which a change from the frequentist to the Bayesian paradigm is recommended. In the former, uncertainty about the unknown parameters is measured by confidence and significance levels, interpreted and calibrated under hypothetical repetition, while probability distributions are attached to the unknown parameters in the Bayesian approach, and the notion of probability is extended to reflect uncertainty of knowledge. In addition, the Bayesian approach can mimic a learning process and reflects the accumulation of knowledge over time. Model averaging is again recommended as the preferred method for estimating the BMD and calculating its credible interval. The set of default models to be used for BMD analysis has been reviewed and amended so that there is now a single set of models for quantal and continuous data. The flow chart guiding the reader step-by-step when performing a BMD analysis has also been updated, and a chapter comparing the frequentist to the Bayesian paradigm inserted. Also, when using Bayesian BMD modelling, the lower bound (BMDL) is to be considered as potential RP, and the upper bound (BMDU) is needed for establishing the BMDU/BMDL ratio reflecting the uncertainty in the BMD estimate. This updated guidance does not call for a general re-evaluation of previous assessments where the NOAEL approach or the BMD approach as described in the 2009 or 2017 Guidance was used, in particular when the exposure is clearly lower (e.g. more than one order of magnitude) than the health-based guidance value. Finally, the SC firmly reiterates to reconsider test guidelines given the wide application of the BMD approach.

EFSA was asked by the European Commission to evaluate synthetic biology (SynBio) developments for agri-food use in the near future and to determine whether or not they are expected to constitute potential new hazards/risks. Moreover, EFSA was requested to evaluate the adequacy of existing guidelines for risk assessment of SynBio and if updated guidance is needed. The scope of this Opinion covers food and feed risk assessment, the variety of microorganisms that can be used in the food/feed chain and the whole spectrum of techniques used in SynBio. This Opinion complements a previously adopted Opinion with the evaluation of existing guidelines for the microbial characterisation and environmental risk assessment of microorganisms obtained through SynBio. The present Opinion confirms that microbial SynBio applications for food and feed use, with the exception of xenobionts, could be ready in the European Union in the next decade. New hazards were identified related to the use or production of unusual and/or new-to-nature components. Fifteen cases were selected for evaluating the adequacy of existing guidelines. These were generally adequate for assessing the product, the production process, nutritional and toxicological safety, allergenicity, exposure and post-market monitoring. The comparative approach and a safety assessment per se could be applied depending on the degree of familiarity of the SynBio organism/product with the non-genetically modified counterparts. Updated guidance is recommended for: (i) bacteriophages, protists/microalgae, (ii) exposure to plant protection products and biostimulants, (iii) xenobionts and (iv) feed additives for insects as target species. Development of risk assessment tools is recommended for assessing nutritional value of biomasses, influence of microorganisms on the gut microbiome and the gut function, allergenic potential of new-to-nature proteins, impact of horizontal gene transfer and potential risks of living cell intake. A further development towards a strain-driven risk assessment approach is recommended.

The EFSA Scientific Committee was asked to provide guidance on the most appropriate in vivo tests to follow up on positive in vitro results for aneugenicity, and on the approach to risk assessment for substances that are aneugenic but not clastogenic nor causing gene mutations. The Scientific Committee confirmed that the preferred approach is to perform an in vivo mammalian erythrocyte micronucleus test with a relevant route of administration. If this is positive, it demonstrates that the substance is aneugenic in vivo. A negative result with evidence that the bone marrow is exposed to the test substance supports a conclusion that aneugenic activity is not expressed in vivo. If there is no evidence of exposure to the bone marrow, a negative result is viewed as inconclusive and further studies are required. The liver micronucleus assay, even though not yet fully validated, can provide supporting information for substances that are aneugenic following metabolic activation. The gastrointestinal micronucleus test, conversely, to be further developed, may help to assess aneugenic potential at the initial site of contact for substances that are aneugenic in vitro without metabolic activation. Based on the evidence in relation to mechanisms of aneugenicity, the Scientific Committee concluded that, in principle, health‐based guidance values can be established for substances that are aneugenic but not clastogenic nor causing gene mutations, provided that a comprehensive toxicological database is available. For situations in which the toxicological database is not sufficient to establish health‐based guidance values, some approaches to risk assessment are proposed. The Scientific Committee recommends further development of the gastrointestinal micronucleus test, and research to improve the understanding of aneugenicity to support risk assessment., This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2021.EN-6814/full

A mandatory national Irish bovine viral diarrhoea (BVD) eradication programme, coordinated by Animal Health Ireland, commenced in 2013. Key decisions and programme review are undertaken by a cross-industry Implementation Group (BVDIG) supported by a Technical Working Group. Ear notch tissue is collected from all new-born calves using modified official identity tags, supplemented by additional blood sampling, including for confirmatory testing of calves with initial positive results and testing of their dams. Testing is delivered by private laboratories in conjunction with the National Reference Laboratory, with all results reported to a central database. This database manages key elements of the programme, issuing results to herdowners by short message service messaging supplemented by letters; assigning and exchanging animal-level statuses with government databases of the Department of Agriculture, Food and the Marine to enable legislated restrictions on animal movements; assigning negative herd status based on test results; generating regular reports for programme management and evaluation and providing herd-specific dashboards for a range of users. Legislation supporting the programme has been in place throughout but has not thus far mandated the slaughter of persistently infected (PI) calves. 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). A framework for funded investigations by PVPs in positive herds was developed to identify plausible sources of infection, to resolve the status of all animals in the herd and to agree up to three measures to prevent re-introduction of the virus. 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. Department of Agriculture, Food and the Marine

Various European Member States have implemented control or eradication programmes for endemic infectious diseases in cattle. The design of these programmes varies between countries and therefore comparison of the outputs of different control programmes is complex. Although output-based methods to estimate the confidence of freedom resulting from these programmes are under development, as yet there is no practical modeling framework applicable to a variety of infectious diseases. Therefore, a data collection tool was developed to evaluate data availability and quality and to collect actual input data required for such a modeling framework. The aim of the current paper is to present the key learnings from the process of the development of this data collection tool. The data collection tool was developed by experts from two international projects: STOC free (Surveillance Tool for Outcome-based Comparison of FREEdom from infection, www.stocfree.eu) and SOUND control (Standardizing OUtput-based surveillance to control Non-regulated Diseases of cattle in the EU, www.sound-control.eu). Initially a data collection tool was developed for assessment of freedom of bovine viral diarrhea virus in six Western European countries. This tool was then further generalized to enable inclusion of data for other cattle diseases i.e., infectious bovine rhinotracheitis and Johne's disease. Subsequently, the tool was pilot-tested by a Western and Eastern European country, discussed with animal health experts from 32 different European countries and further developed for use throughout Europe. The developed online data collection tool includes a wide range of variables that could reasonably influence confidence of freedom, including those relating to cattle demographics, risk factors for introduction and characteristics of disease control programmes. Our results highlight the fact that data requirements for different cattle diseases can be generalized and easily included in a data collection tool. However, there are large differences in data availability and comparability across European countries, presenting challenges to the development of a standardized data collection tool and modeling framework. These key learnings are important for development of any generic data collection tool for animal disease control purposes. Further, the results can facilitate development of output-based modeling frameworks that aim to calculate confidence of freedom from disease. European Food Safety Authority (EFSA) Dutch Ministry of Agriculture, Nature and Food Quality

In response to the coronavirus (COVID-19) outbreak, the Irish Epidemiological Modelling Advisory Group (IEMAG) for COVID-19 was established to assist the Irish National Public Health Emergency Team (NPHET) in their decision-making during the pandemic. A subcommittee from IEMAG (the epidemiological parameters team) was tasked with researching the various parameters, leading to the development of a series of synthesis documents relevant to the parameterisation of a COVID-19 transmission model for Ireland. These parameters include: • R0/R • Latent period & relative importance of pre-symptomatic period • Incubation period • Generation time & serial interval • Proportion of infected who are asymptomatic, by age • Length of infectious period in asymptomatic people and in symptomatic people who do not isolate • Time from onset of symptoms to diagnosis/test results and to hospitalisation • Length of hospital stay and admission to ICUs • Relative infectiousness of asymptomatic versus symptomatic infected people. The current document presents an up-to-date summary of these synthesis documents. A further synthesis document on age-related susceptibility and age-related infectiousness is in preparation.

This Guidance document describes harmonised risk assessment methodologies for combined exposure to multiple chemicals for all relevant areas within EFSA's remit, i.e. human health, animal health and ecological areas. First, a short review of the key terms, scientific basis for combined exposure risk assessment and approaches to assessing (eco)toxicology is given, including existing frameworks for these risk assessments. This background was evaluated, resulting in a harmonised framework for risk assessment of combined exposure to multiple chemicals. The framework is based on the risk assessment steps (problem formulation, exposure assessment, hazard identification and characterisation, and risk characterisation including uncertainty analysis), with tiered and stepwise approaches for both whole mixture approaches and component‐based approaches. Specific considerations are given to component‐based approaches including the grouping of chemicals into common assessment groups, the use of dose addition as a default assumption, approaches to integrate evidence of interactions and the refinement of assessment groups. Case studies are annexed in this guidance document to explore the feasibility and spectrum of applications of the proposed methods and approaches for human and animal health and ecological risk assessment. The Scientific Committee considers that this Guidance is fit for purpose for risk assessments of combined exposure to multiple chemicals and should be applied in all relevant areas of EFSA's work. Future work and research are recommended., This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2019.EN-1589/full, http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2019.EN-1602/full

Over recent decades, changes in agriculture have pushed animal welfare as a topic of concern into mainstream public, policy and political conversations (Buller and Morris, 2003; Fraser, 2014; Broom, 2016). Despite the relationship between farmers and farm animals being important for farm animal welfare standards, there is limited understanding of how the nature of this relationship influences welfare outcomes. Understanding the complexities of this relationship and the wider context in which these complexities are situated is central to forming and implementing interventions that can be effective in improving farm animal welfare on individual farms. Department of Agriculture, Food and the Marine

Veterinary Council of Ireland Deposited by bulk import

World Horse Welfare Deposited by bulk import

The Footrot Strategic Plan (FSP) aims to progressively eradicate non-benign footrot in sheep from New South Wales. All but a small portion of the drier regions of NSW is now gazetted with Protected Area status - placing legal requirements on farmers and relevant authorities in relation to disease notification and, where disease exists, farm quarantine and disease eradication. The author's experience from north western NSW suggests, however, that despite these legal requirements, many local producers would be unlikely to notify upon suspecting disease. Furthermore, of those producers with properties quarantined for footrot during the period 1990-1992 in the Coonamble Rural Lands Protection Board, almost half lacked a real commitment to footrot eradication.Research towards improving the FSP and related programs has been dominated by methods to overcome technical obstacles. In non-endemic regions of NSW, such as the north west, however, major constraints on the FSP include problems of an economic or social nature. This paper discusses some constraints limiting the acceptance and adoption of the FSP in the Coonamble region of NSW and identifies some possible solutions to these problems.

The Department of Agriculture, Food and the Marine (DAFM) provides ongoing financial support to two research units within the UCD School of Veterinary Medicine at University College Dublin: The UCD Centre for Veterinary Epidemiology and Risk Analysis (UCD CVERA); and The TB Diagnostics and Immunology Research Laboratory. These units each work to support DAFM policy, inspectorate and laboratory staff in the area of animal health. UCD CVERA is a national resource centre, providing policy advice and conducting epidemiological research on a wide range of animal health issues. In addition, UCD CVERA provides general support to government, industry and the veterinary profession (pre- and post-graduation). The TB Diagnostics and Immunology Research Laboratory focuses on bovine and badger tuberculosis research. This report documents work conducted by, or in association with, these UCD-based research units during 2020 and 2021. Dept. of Agriculture Fisheries & Food (DAFF)

The Department of Agriculture, Food and the Marine (DAFM) provides ongoing financial support to two research units within the UCD School of Veterinary Medicine at University College Dublin: - The UCD Centre for Veterinary Epidemiology and Risk Analysis (UCD CVERA); and - The TB Diagnostics and Immunology Research Laboratory. These units each work to support DAFM policy, inspectorate and laboratory staff in the area of animal health. The TB Diagnostics and Immunology Research Laboratory focuses on bovine tuberculosis research. UCD CVERA is a national resource centre, providing policy advice and conducting epidemiological research on a wide range of animal health issues. In addition, UCD CVERA provides general support to government, industry and the veterinary profession (pre- and post-graduation). This report documents work conducted by, or in association with, these UCD-based research units during 2018 and 2019. Department of Agriculture, Food and the Marine

The UCD Centre for Veterinary Epidemiology and Risk Analysis (UCD CVERA) is the national resource centre for veterinary epidemiology in Ireland, located within the UCD School of Veterinary Medicine at University College Dublin. The Centre was initially established as the Tuberculosis Investigation Unit, but has since broadened its remit to cover a wide range of international, national and local animal health matters, including: Epidemiological support for the control and eradication of regulatory animal diseases, including the national eradication programme for bovine tuberculosis, and for emergency animal disease preparedness and response; Work in support of Animal Health Ireland (www.animalhealthireland.ie), which is providing a proactive, coordinated and industry-led approach in Ireland to non-regulatory animal health concerns (such as mastitis, bovine viral diarrhoea and Johne’s disease); and Epidemiological support for a broad range of other animal health and welfare issues relating to animal health surveillance, on-farm investigations, welfare of farmed livestock and horses, health of companion animals and farmed fish, and international collaboration. UCD CVERA staff work closely with national policy-makers, both in government and industry. Staff also contribute to training in veterinary medicine, both to undergraduates and postgraduates. A broad range of expertise is represented within the Centre, including database development and management, geographic information systems, statistics, veterinary medicine and epidemiology. The Centre is staffed by employees of University College Dublin and of the Department of Agriculture, Food and the Marine (DAFM). During 2017, a strategic review of CVERA took place in conjunction with the Department of Agriculture, Food and the Marine, the UCD School of Veterinary Medicine, Animal Health Ireland and other stakeholders. As a result of the review, CVERA has developed clearly defined strategic goals, objectives and expected outcomes for the medium term. These are presented in the CVERA Statement of Strategy 2017-20. Three priority areas have been identified for immediate action, including the establishment of an independent management board, the introduction of systems to improve task management within CVERA, and a communications plan. Department of Agriculture, Food and the Marine The Report contains abstracts from journal papers. A large number of the journals papers are open access. I used Rightslink and the CCC to acquire permission to reprint the abstracts of the non-open access papers. Permission statements appear with each of the abstracts where required.

The UCD Centre for Veterinary Epidemiology and Risk Analysis (UCD CVERA) is the national resource centre for veterinary epidemiology in Ireland, located within the UCD School of Veterinary Medicine at University College Dublin. The Centre was initially established as the Tuberculosis Investigation Unit, but in recent years has broadened its remit to cover a wide range of international, national and local animal health matters, including: - Epidemiological support for the control and eradication of regulatory animal diseases, including the national eradication programme for bovine tuberculosis; - Work in support of Animal Health Ireland (www.animalhealthireland.ie), which is providing a proactive, coordinated and industry-led approach in Ireland to non-regulatory animal health concerns (such as mastitis, bovine viral diarrhoea and Johne’s disease); and - Epidemiological support for a broad range of other animal health and welfare issues relating to emergency animal disease preparedness and response (for example, Schmallenberg viral infection), on-farm investigations, welfare of farmed livestock and horses, health of companion animals and farmed fish, and international collaboration. UCD CVERA staff work closely with national policy-makers, both in government and industry. Staff also contribute to training in veterinary medicine, both to undergraduates and postgraduate. A broad range of expertise is represented within the Centre, including database development and management, geographic information systems, statistics, veterinary medicine and epidemiology. The Centre is staffed by employees of University College Dublin and of the Department of Agriculture, Food and the Marine (DAFM). The badger vaccine project is a programme of research with the objective to develop a vaccine to control tuberculosis in badgers and to break the link of infection to cattle. Over the course of nine studies with captive badgers, we have demonstrated as proof of principle that vaccination of badgers with BCG by a number of routes, including oral delivery, generates high levels of protective immunity against challenge with M. bovis. We are continuing to carry out studies with captive population of badgers to refine the vaccine and address issues relating to licensing of the vaccine as a veterinary medicine. Department of Agriculture, Food and the Marine

The UCD Centre for Veterinary Epidemiology and Risk Analysis (UCD CVERA) is the national resource centre for veterinary epidemiology in Ireland, located within the UCD School of Veterinary Medicine at University College Dublin. The Centre was initially established as the Tuberculosis Investigation Unit, but in recent years has broadened its remit to cover a wide range of international, national and local animal health matters, including: - Epidemiological support for the control and eradication of regulatory animal diseases, including the national eradication programme for bovine tuberculosis; - Work in support of Animal Health Ireland (www.animalhealthireland.ie), which is providing a proactive, coordinated and industry-led approach in Ireland to non-regulatory animal health concerns (such as mastitis, bovine viral diarrhoea and Johne’s disease); and - Epidemiological support for a broad range of other animal health and welfare issues relating to emergency animal disease preparedness and response (for example, avian influenza, bluetongue and equine infectious anaemia), on-farm investigations, welfare of farmed livestock and horses, health of companion animals and farmed fish, and international collaboration. UCD CVERA staff work closely with national policy-makers, both in government and industry. Staff also contribute to training in veterinary medicine, both to undergraduates and postgraduate. A broad range of expertise is represented within the Centre, including database development and management, geographic information systems, statistics, veterinary medicine and epidemiology. The Centre is staffed by employees of University College Dublin and of the Department of Agriculture, Food and the Marine (DAFM). The badger vaccine project is a programme of research with the objective to develop a vaccine to control tuberculosis in badgers and to break the link of infection to cattle. In studies with captive badgers, we have demonstrated that vaccination of badgers with BCG by a number of routes, including oral delivery, generates high levels of protective immunity against challenge with M. bovis. We are continuing to carry out studies with captive population of badgers to refine the vaccine and address issues relating to the eventual licensing of the vaccine as a veterinary medicine. In our most recent captive badger study, the preliminary analysis of data indicates that lower doses of oral BCG vaccine (10^5 colony forming units) are just as effective at protecting badgers against experimental challenge, compared with the standard dose (10^7 colony forming units). This may have important implications for cost of manufacture of an oral vaccine. The vaccine field trial, which commenced in 2009 to test the efficacy of the oral BCG vaccine in free-living badgers over a wide geographic area in Co. Kilkenny, is nearing completion. The vaccination phase of the field trial finished in 2012, and 273 badgers have since been removed from the site for detailed post-mortem analysis. The analysis of the data has commenced and it is hoped to present preliminary results early in 2014. Department of Agriculture, Food and the Marine

Department of Agriculture, Food and the Marine Deposited by bulk import

Department of Agriculture, Food and the Marine Deposited by bulk import

Department of Agriculture, Food and the Marine Deposited by bulk import