Guidance on protocol development for EFSA generic scientific assessments.

EFSA Strategy 2027 outlines the need for fit-for-purpose protocols for EFSA generic scientific assessments to aid in delivering trustworthy scientific advice. This EFSA Scientific Committee guidance document helps address this need by providing a harmonised and flexible framework for developing protocols for EFSA generic assessments. The guidance replaces the 'Draft framework for protocol development for EFSA's scientific assessments' published in 2020. The two main steps in protocol development are described. The first is problem formulation, which illustrates the objectives of the assessment. Here a new approach to translating the mandated Terms of Reference into scientifically answerable assessment questions and sub-questions is proposed: the 'APRIO' paradigm (Agent, Pathway, Receptor, Intervention and Output). Owing to its cross-cutting nature, this paradigm is considered adaptable and broadly applicable within and across the various EFSA domains and, if applied using the definitions given in this guidance, is expected to help harmonise the problem formulation process and outputs and foster consistency in protocol development. APRIO may also overcome the difficulty of implementing some existing frameworks across the multiple EFSA disciplines, e.g. the PICO/PECO approach (Population, Intervention/Exposure, Comparator, Outcome). Therefore, although not mandatory, APRIO is recommended. The second step in protocol development is the specification of the evidence needs and the methods that will be applied for answering the assessment questions and sub-questions, including uncertainty analysis. Five possible approaches to answering individual (sub-)questions are outlined: using evidence from scientific literature and study reports; using data from databases other than bibliographic; using expert judgement informally collected or elicited via semi-formal or formal expert knowledge elicitation processes; using mathematical/statistical models; and - not covered in this guidance - generating empirical evidence ex novo. The guidance is complemented by a standalone 'template' for EFSA protocols that guides the users step by step through the process of planning an EFSA scientific assessment.

Prioritisation of zoonotic diseases for coordinated surveillance systems under the One Health approach for cross-border pathogens that threaten the Union.

In the context of the initiative 'CP-g-22-04.01 Direct grants to Member States' authorities', EFSA was requested to develop and conduct a prioritisation of zoonotic diseases, in collaboration with Member States, to identify priorities for the establishment of a coordinated surveillance system under the One Health approach. The methodology developed by EFSA's Working Group on One Health surveillance was based on a combination of multi-criteria decision analysis and the Delphi method. It comprised the establishment of a list of zoonotic diseases, definition of pathogen- and surveillance-related criteria, weighing of those criteria, scoring of zoonotic diseases by Member States, calculation of summary scores, and ranking of the list of zoonotic diseases according to those scores. Results were presented at EU and country level. A prioritisation workshop was organised with the One Health subgroup of EFSA's Scientific Network for Risk Assessment in Animal Health and Welfare in November 2022 to discuss and agree on a final list of priorities for which specific surveillance strategies would be developed. Those 10 priorities were Crimean-Congo haemorrhagic fever, echinococcosis (both E. granulosus and E. multilocularis), hepatitis E, influenza (avian), influenza (swine), Lyme borreliosis, Q-fever, Rift Valley fever, tick-borne encephalitis and West Nile fever. 'Disease X' was not assessed in the same way as other zoonotic diseases on the list, but it was added to the final list of priorities due to its relevance and importance in the One Health context.

Coordinated surveillance system under the One Health approach for cross-border pathogens that threaten the Union - options for sustainable surveillance strategies for priority pathogens.

This report provides guidance for Member states who plan to submit applications under the work programme 'CP-g-22-04.01 Direct grants to Member States' authorities'. The priority pathogens on which the coordinated surveillance under the grant initiative shall focus have been identified in a prioritisation exercise with Member States and ECDC. These are Crimean Congo haemorrhagic fever, echinococcosis, hepatitis E, highly pathogenic avian influenza (HPAI), influenza in swine, Lyme disease, Q-fever, Rift Valley fever, tick-borne encephalitis, West Nile fever and Disease X (Disease Y of animals). Surveillance activities (surveillance cards) have been proposed for these agents in this report. Member States should select one or more diseases from the list of priority diseases and then choose surveillance activities from the surveillance cards and modify them where needed, to reflect their national needs and situation. Member States can also design alternative surveillance activities for the priority infectious agents that may better fit the epidemiological situation in their country. Further, this report provides a section on surveillance perspectives that links infectious agents to different hosts, allowing Member States to consider the testing for multiple infectious agents in samples from a single host population, as well as sections providing guidance on surveillance in vectors and wildlife and for Disease X (Disease Y in animals). Member States are encouraged to develop cross-sectoral collaborations and the report provides guidance on cross-sectoral collaboration to help them. Finally, there is a roadmap providing an overall description of the steps in the process of developing a surveillance system in order to apply for the grant.

Assessment of the control measures of the Category A diseases of the Animal Health Law: prohibitions in restricted zones and risk-mitigating treatments for products of animal origin and other materials.

EFSA received a mandate from the European Commission to assess the effectiveness of prohibitions of certain activities in restricted zones, and of certain risk mitigation treatments for products of animal origin and other materials with respect to diseases included in the Category A list in the Animal Health Law (Regulation (EU) 2016/429). This opinion belongs to a series of opinions where other disease-specific control measures have been assessed. In this opinion, EFSA and the AHAW Panel of experts review the effectiveness of (i) prohibiting the movements of certain products, notably germinal products (semen, oocytes, embryos and hatching eggs), products of animal origin and animal by-products and feed of plant origin, hay and straw, and (ii) risk mitigation treatments for products of animal origin. In terms of semen, oocytes, embryos and hatching eggs, it was agreed that there was a lack of evidence particularly for embryos and oocytes reflected in a varying degree of uncertainty, whether these commodities could potentially contain the pathogen under consideration. The scenario assessed did not consider whether the presence of pathogen would lead to infection in the recipient animal. In terms of animal products, certain animal by-products and movement of feed of plant origin and straw, the assessment considered the ability of the commodity to transmit disease to another animal if exposed. For most pathogens, products were to some degree considered a risk, but lack of field evidence contributed to the uncertainty, particularly as potential exposure of ruminants to meat products is concerned. In terms of the risk mitigating treatments, recommendations have been made for several of these treatments, because the treatment description is not complete, the evidence is poor or inconclusive, or the evidence points to the treatment being ineffective.

Guidance on good practice in conducting scientific assessments in animal health using modelling.

The EFSA asked the Panel on Animal Health and Welfare to develop a guidance document on good practice in conducting scientific assessments in animal health using modelling. In previous opinions, the AHAW Panel has responded to two-thirds of animal health-related mandates using some kind of modelling. These models range from simple to complex, employing a combination of scientific, economic, socio-economic or other types of data. Hence, there is strong interest in the development of a guidance document to integrate modelling efforts into the routine process of EFSA working groups. In this document, an 'operating procedure' (OP) for the use of modelling within an AH working group is presented. The OP provides a detailed flowchart enabling modelling to be transparently and consistently integrated in the assessment. The OP is structured into phases. These phases combine the relevant standard operating procedures and working instructions of EFSA with the modelling process. Each phase includes roles and actions to be taken, expected output and the sequence of agreements that need to be made between all partners in the scientific assessment. In conclusion, it is expected that adherence to the OP will improve transparency of models in EFSA outputs, and it is recommended to adopt it as a standard procedure when responding to AHAW mandates.

Assessment of the control measures of category A diseases of the Animal Health Law: Infection with rinderpest virus (Rinderpest).

EFSA received a mandate from the European Commission to assess the effectiveness of control measures against diseases included in the Category A list according to Regulation (EU) 2016/429 on transmissible animal diseases ('Animal Health Law'). This opinion belongs to a series of opinions where these control measures are assessed, with this opinion covering the assessment of control measures for rinderpest (RP), the only animal disease to have been globally eradicated. In this opinion, the AHAW Panel reviewed the effectiveness of: (i) clinical and laboratory sampling procedures, (ii) monitoring period and (iii) the minimum radius of the protection and surveillance zone, and the minimum length of time the measures should be applied in these zones. The general methodology used for this series of opinions has been published elsewhere. The transmission kernels used for the assessment of the minimum radius of the protection and surveillance zones are shown. Several scenarios for which control measures had to be assessed were agreed prior to the assessment. Considering that RP has been eradicated globally, a re-emergence that is not stopped in its early phases could have a devastating impact on animal health and the economy. The panel concludes that no suitable strategies are available to entirely mitigate the risk associated with granting derogations from killing of animals in an affected establishment or for animal movements. Therefore, the panel recommends to not grant any derogations. The monitoring period of 21 days was assessed as effective, except for the hypothetical first re-emergence of RP, when lack of awareness and diagnostic capability may extend the time to detection. It was concluded that the protection and the surveillance zones would contain 90% and > 99%, respectively, of the infections from an affected establishment. Enlarging the protection zone to 4 km would contain the disease spread with 95% probability.

African swine fever and outdoor farming of pigs.

This opinion describes outdoor farming of pigs in the EU, assesses the risk of African swine fewer (ASF) introduction and spread associated with outdoor pig farms and proposes biosecurity and control measures for outdoor pig farms in ASF-affected areas of the EU. Evidence was collected from Member States (MSs) veterinary authorities, farmers' associations, literature and legislative documents. An Expert knowledge elicitation (EKE) was carried out to group outdoor pig farms according to their risk of introduction and spread of ASF, to rank biosecurity measures regarding their effectiveness with regard to ASF and propose improvements of biosecurity for outdoor pig farming and accompanying control measures. Outdoor pig farming is common and various farm types are present throughout the EU. As there is no legislation at European level for categorising outdoor pig farms in the EU, information is limited, not harmonised and needs to be interpreted with care. The baseline risk of outdoor pig farms for ASFV introduction and its spread is high but with considerable uncertainty. The Panel is 66-90% certain that, if single solid or double fences were fully and properly implemented on all outdoor pig farms in areas of the EU where ASF is present in wild boar and in domestic pigs in indoor farms and outdoor farms (worst case scenario not considering different restriction zones or particular situations), without requiring any other outdoor-specific biosecurity measures or control measures, this would reduce the number of new ASF outbreaks occurring in these farms within a year by more than 50% compared to the baseline risk. The Panel concludes that the regular implementation of independent and objective on-farm biosecurity assessments using comprehensive standard protocols and approving outdoor pig farms on the basis of their biosecurity risk in an official system managed by competent authorities will further reduce the risk of ASF introduction and spread related to outdoor pig farms.

Ability of different matrices to transmit African swine fever virus.

This opinion assesses the risk posed by different matrices to introduce African swine fever virus (ASFV) to non-affected regions of the EU. Matrices assessed are feed materials, enrichment/bedding materials and empty live pigs transport vehicles returning from affected areas. Although the risk from feed is considered to be lower than several other pathways (e.g. contact with infected live animals and swill feeding), it cannot be ruled out that matrices assessed in this opinion pose a risk. Evidence on survival of ASFV in different matrices from literature and a public consultation was used in an Expert Knowledge Elicitation (EKE) on the possible contamination of products and traded or imported product volumes used on pig farms. The EKE results were used in a model that provided a risk-rank for each product's contamination likelihood ('q'), its trade or import volume from affected EU or Eurasian areas (N) and the modelled number of potentially infected pig farms (N × q). The products ranking higher regardless of origin or destination were mash and pelleted compound feed, feed additives and cereals. Bedding/enrichment materials, hydrolysed proteins and blood products ranked lowest regardless of origin or destination. Empty vehicles ranked lower than compound feed but higher than non-compound feed or bedding/enrichment material. It is very likely (95-99% certainty) that compound feed and cereals rank higher than feed materials, which rank higher than bedding/enrichment material and forage. As this is an assessment based on several parameters including the contamination and delivery to a pig farm, all of which have the same impact on the final ranking, risk managers should consider how the relative rank of each product may change with an effective storage period or a virus inactivation step.

Draft for internal testing Scientific Committee guidance on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments.

EFSA requested its Scientific Committee to prepare a guidance document on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments. The guidance document provides an introduction to epidemiological studies and illustrates the typical biases of the different epidemiological study designs. It describes key epidemiological concepts relevant for evidence appraisal. Regarding study reliability, measures of association, exposure assessment, statistical inferences, systematic error and effect modification are explained. Regarding study relevance, the guidance describes the concept of external validity. The principles of appraising epidemiological studies are illustrated, and an overview of Risk of Bias (RoB) tools is given. A decision tree is developed to assist in the selection of the appropriate Risk of Bias tool, depending on study question, population and design. The customisation of the study appraisal process is explained, detailing the use of RoB tools and assessing the risk of bias in the body of evidence. Several examples of appraising experimental and observational studies using a Risk of Bias tool are annexed to the document to illustrate the application of the approach. This document constitutes a draft that will be applied in EFSA's assessments during a 1-year pilot phase and be revised and complemented as necessary. Before finalisation of the document, a public consultation will be launched.

Associations between animal welfare indicators and Campylobacter spp. in broiler chickens under commercial settings: A case study.

Few studies have previously investigated how poor animal welfare might be associated with infection of zoonotic pathogens in humans. This paper assesses the predictive value of the presence of Campylobacter spp. in broiler chicken flocks when animal-based measures related to footpad dermatitis, hock burns, body lesions and arthritis are identified under commercial conditions (high density). The study population included 32 flocks analysed on farm and at slaughter, slaughtered between April and August 2008 in six different slaughter plants in Brittany, France. Welfare and health indicators are those indicated by the European legislation and sampling was carried out in the framework of the European baseline survey on the prevalence of Campylobacter in broiler chicken. Caecal contents, sampled both on farm and at slaughter, and carcass skin samples from the neck and breast at slaughter, were investigated for the presence of Campylobacter spp. Logistic models/classification trees were used to estimate the probability of the presence (or absence) of a specific foodborne pathogen in a flock based on specific animal-based measures (or combinations of measures) in order to study the potential relationship between welfare indicators and foodborne pathogen prevalence/incidence levels. On farm, flocks with more than 25% animals with severe lesions on between 25 and 50% of the footpad are predicted to be Campylobacter-positive whereas flocks where less than 13 individuals have arthritis are predicted to be Campylobacter-negative. The error rate on farm and at slaughter was 10 and 4% respectively indicating good predicting abilities. A poor welfare environment may result in stress, which reduces chicken immunocompetence making them more susceptible to Campylobacter spp. An infection with Campylobacter spp may lead to impaired defence and susceptibility to other pathogens which may result in greater intestinal excretion. Poor welfare and high growing rate lead to digestive troubles that lead to litter humidity. Litter humidity that, among other things, causes footpad dermatitis may also influence the horizontal transmission of the Campylobacter spp. infection due to the normal coprophagic behaviour of poultry. Reducing welfare problems by a better management of rearing conditions would not only improve broiler welfare, but it would also decrease the risks of Campylobacter contamination, of carcass condemnations and of economic loss for the poultry industry.

West Nile virus surveillance in Europe: moving towards an integrated animal-human-vector approach.

This article uses the experience of five European countries to review the integrated approaches (human, animal and vector) for surveillance and monitoring of West Nile virus (WNV) at national and European levels. The epidemiological situation of West Nile fever in Europe is heterogeneous. No model of surveillance and monitoring fits all, hence this article merely encourages countries to implement the integrated approach that meets their needs. Integration of surveillance and monitoring activities conducted by the public health authorities, the animal health authorities and the authorities in charge of vector surveillance and control should improve efficiency and save resources by implementing targeted measures. The creation of a formal interagency working group is identified as a crucial step towards integration. Blood safety is a key incentive for public health authorities to allocate sufficient resources for WNV surveillance, while the facts that an effective vaccine is available for horses and that most infected animals remain asymptomatic make the disease a lesser priority for animal health authorities. The examples described here can support other European countries wishing to strengthen their WNV surveillance or preparedness, and also serve as a model for surveillance and monitoring of other (vector-borne) zoonotic infections.

Scientific and technical assistance concerning the survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU.

A new fungus, Batrachochytrium salamandrivorans (Bsal), was identified in wild populations of salamanders in the Netherlands and Belgium, and in kept salamander populations in Germany and the United Kingdom. EFSA assessed the potential of Bsal to affect the health of wild and kept salamanders in the EU, the effectiveness and feasibility of a movement ban of traded salamanders, the validity, reliability and robustness of available diagnostic methods for Bsal detection, and possible alternative methods and feasible risk mitigation measures to ensure safe international and EU trade of salamanders and their products. Bsal was isolated and characterised in 2013 from a declining fire salamander (Salamandra salamandra) population in the Netherlands. Based on the available evidence, it is likely that Bsal is a sufficient cause for the death of S. salamandra both in the laboratory and in the wild. Despite small sample sizes, the available experimental evidence indicates that Bsal is associated with disease and death in individuals of 12 European and 3 Asian salamander species, and with high mortality rate outbreaks in kept salamanders. Bsal experimental infection was detected in individuals of at least one species pertaining to the families Salamandridae, Plethodontidae, Hynobiidae and Sirenidae. Movement bans constitute key risk mitigation measures to prevent pathogen spread into naïve areas and populations. The effectiveness of a movement ban is mainly dependent on the import volumes, possibility of Bsal to remain viable outside susceptible/tolerant species, and the capacity to limit illegal movements. Duplex real-time PCR can be used to detect Bsal DNA, but has not been fully validated. Quarantining salamanders, enacting legislation that requires testing of animals to demonstrate freedom from Bsal, before movement can take place, restricting salamander movements, tracking all traded species, hygienic procedures/biosecurity measures before and during movements, and increasing public awareness are relevant measures for ensuring safe intra-EU and international trade of salamanders.

Epidemiological analyses on African swine fever in the Baltic countries and Poland.

African swine fever virus (ASFV) has been notified in the Baltic countries and the eastern part of Poland from the beginning of 2014 up to now. In collaboration with the ASF-affected Member States (MS), EFSA is updating the epidemiological analysis of ASF in the European Union which was carried out in 2015. For this purpose, the latest epidemiological and laboratory data were analysed in order to identify the spatial-temporal pattern of the epidemic and a risk factors facilitating its spread. Currently, the ASF outbreaks in wild boar in the Baltic countries and Poland can be defined as a small-scale epidemic with a slow average spatial spread in wild boar subpopulations (approximately from 1 in Lithuania and Poland to 2 km/month in Estonia and Latvia). The number of positive samples in hunted wild boar peaks in winter which can be explained by human activity patterns (significant hunting activity over winter). The number of positive samples in wild boar found dead peaks in summer. This could be related to the epidemiology of the disease and/or the biology of wild boar; however, this needs further investigation. Virus prevalence in hunted wild boar is very low (0.04-3%), without any apparent trend over time. Apparent virus prevalence at country level in wild boar found dead in affected countries ranges from 60% to 86%, with the exception of Poland, where values between 0.5% and 1.42%, were observed. Since the beginning of the epidemic, the apparent antibody prevalence in hunted wild boar has always been lower than the apparent virus prevalence, indicating an unchanged epidemiological/immunological situation. The risk factor analysis shows an association between the number of settlements, human and domestic pigs population size or wild boar population density and the presence of ASF in wild boar for Estonia, Latvia and Lithuania.

Ad hoc method for the assessment on listing and categorisation of animal diseases within the framework of the Animal Health Law.

The European Commission has requested EFSA to assess animal diseases according to the criteria as laid down in Articles 5, 7, 8 and Annex IV for the purpose of categorisation of diseases in accordance with Article 9 of the Regulation (EU) No 2016/429 (Animal Health Law). This scientific opinion addresses the ad hoc method developed for assessing any animal disease for the listing and categorisation of diseases within the Animal Health Law (AHL) framework. The assessment of individual diseases is addressed in distinct scientific opinions that are published separately. The assessment of Articles 5, 8 and 9 criteria is performed on the basis of the information collected according to Article 7 criteria. For that purpose, Article 7 criteria were structured into parameters and the information was collected at parameter level. The resulting fact sheets on the profile and impact of each disease were compiled by disease scientists. A mapping was developed to identify which parameters from Article 7 were needed to inform each Article 5, 8 and 9 criterion. Specifically, for Articles 5 and 9 criteria, a categorical assessment was performed, by applying an expert judgement procedure, based on the mapped information. The judgement was performed by EFSA Panel experts on Animal Health and Welfare in two rounds, individual and collective judgement. The output of the expert judgement on the criteria of Articles 5 and 9 for each disease is composed by the categorical answer, and for the questions where no consensus was reached, the different supporting views are reported.

Expert opinion based modelling of the risk of human infection with H5N1 through the consumption of poultry meat in Germany.

According to current scientific opinion the risk of human infection with H5N1 via preparation and consumption of poultry meat is negligible.This opinion has not yet been challenged by a formal risk assessment, due to the lack of empirical data. We have developed a scenario pathway model as a conceptual framework for a formal assessment of the H5N1 risk to humans through consumption of poultry meat and parameterise the model using information derived from expert opinions. The aim of this study was to investigate whether the notion of an overall negligible risk via the oral infection route is consistent with ad hoc data and expert opinions on the relevant parameters of the model. The model is mainly based on expert opinion. A stochastic Monte-Carlo simulation was conducted which took into consideration (amongst others) the exposure and infection of chicken (broiler and layer), turkeys, ducks and geese, the probabilities of detection prior to slaughter, virus survival and contamination during slaughter, as well as during the cutting and preparation of meat in commercial plants and in private households, respectively. The empirical consumption pattern for poultry meat in Germany was taken into account in the simulation. The results show that the risk for the individual consumer is practically zero whereas up to 23 cases per year in Germany might occur if the upper (more pessimistic) ranges of the expert opinions apply. The finding of a low but non-negligible risk to the population is discussed in relation to the epidemiological information available from recent outbreaks in South East Asia.

Late vaccination reinforcement during a measles epidemic in Niamey, Niger (2003-2004).

Low measles vaccination coverage (VC) leads to recurrent epidemics in many African countries. We describe VC before and after late reinforcement of vaccination activities during a measles epidemic in Niamey, Niger (2003-2004) assessed by Lot Quality Assurance Sampling (LQAS). Neighborhoods of Niamey were grouped into 46 lots based on geographic proximity and population homogeneity. Before reinforcement activities, 96% of lots had a VC below 70%. After reinforcement, this proportion fell to 78%. During the intervention 50% of children who had no previous record of measles vaccination received their first dose (vaccination card or parental recall). Our results highlight the benefits and limitations of vaccine reinforcement activities performed late in the epidemic.