SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control.

The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.

Cross-Validation of Generic Risk Assessment Tools for Animal Disease Incursion Based on a Case Study for African Swine Fever.

In recent years, several generic risk assessment (RA) tools have been developed that can be applied to assess the incursion risk of multiple infectious animal diseases allowing for a rapid response to a variety of newly emerging or re-emerging diseases. Although these tools were originally developed for different purposes, they can be used to answer similar or even identical risk questions. To explore the opportunities for cross-validation, seven generic RA tools were used to assess the incursion risk of African swine fever (ASF) to the Netherlands and Finland for the 2017 situation and for two hypothetical scenarios in which ASF cases were reported in wild boar and/or domestic pigs in Germany. The generic tools ranged from qualitative risk assessment tools to stochastic spatial risk models but were all parameterized using the same global databases for disease occurrence and trade in live animals and animal products. A comparison of absolute results was not possible, because output parameters represented different endpoints, varied from qualitative probability levels to quantitative numbers, and were expressed in different units. Therefore, relative risks across countries and scenarios were calculated for each tool, for the three pathways most in common (trade in live animals, trade in animal products, and wild boar movements) and compared. For the 2017 situation, all tools evaluated the risk to the Netherlands to be higher than Finland for the live animal trade pathway, the risk to Finland the same or higher as the Netherlands for the wild boar pathway, while the tools were inconclusive on the animal products pathway. All tools agreed that the hypothetical presence of ASF in Germany increased the risk to the Netherlands, but not to Finland. The ultimate aim of generic RA tools is to provide risk-based evidence to support risk managers in making informed decisions to mitigate the incursion risk of infectious animal diseases. The case study illustrated that conclusions on the ASF risk were similar across the generic RA tools, despite differences observed in calculated risks. Hence, it was concluded that the cross-validation contributed to the credibility of their results.

Effects of control measures on the spread of LA-MRSA among Danish pig herds between 2006 and 2015 - a simulation study.

There has been a rapid increase in Danish pig herds testing positive for livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA) since the first screening in 2008. Despite a national action plan to control LA-MRSA in the Danish pig population, 88% of pig herds tested positive in a 2016 cross-sectional study of 57 herds. The national action plan was initiated in April 2015 and aimed to reduce the spread of LA-MRSA among pig herds. However, its success is uncertain. We used a simulation model mimicking the spread of LA-MRSA among pig herds between 2006 and 2015 to evaluate the impact of control strategies if these had these been implemented in 2007 or 2010. The strategies were combinations of the following control measures: (1) a reduced number of herds using high-risk antibiotics, (2) a reduced probability of indirect transmission among herds via humans, (3) movement restrictions, and (4) voluntary eradication in 5-7.5% of the herds. Almost all tested control strategies simulated a reduction in the spread of LA-MRSA. The combination of two, three or four intervention strategies showed additive effects and led to larger reductions in the predicted herd prevalence. In addition, the prevalence of LA-MRSA-positive herds at the time when control measures were initiated influenced the effects of the control strategies. Combining the simulated control measures can be considered in future action plans to control LA-MRSA.

Risk assessment of African swine fever in the south-eastern countries of Europe.

The European Commission requested EFSA to estimate the risk of spread of African swine fever (ASF) and to identify potential risk factors (indicators) for the spread of ASF, given introduction in the south-eastern countries of Europe (region of concern, ROC), namely Albania, Bosnia and Herzegovina, Croatia, Greece, Kosovo, Montenegro, North Macedonia, Serbia and Slovenia. Three EU Member States (MS) - Croatia, Greece and Slovenia - were included in the ROC due to their geographical location and ASF-free status. Based on collected information on potential risk factors (indicators) for each country and the relevant EU regulations in force, the estimated probability of spread of ASF within the ROC within one year after introduction into the ROC was assessed to be very high (from 66% to 100%). This estimate was determined after considering the high number of indicators present in most of the countries in the ROC and the known effect that these indicators can have on ASF spread, especially those related to the structure of the domestic pig sector, the presence of wild boar and social factors. The presence of indicators varies between countries in the ROC. Each country is at risk of ASF spread following introduction; however, some countries may have a higher probability of ASF spread following introduction. In addition, the probability of ASF spread from the ROC to EU MSs outside the ROC within one year after introduction of ASF in the ROC was estimated to be very low to low (from 0% to 15%). This estimate was based on the comparison of the indicators present in the ROC and the already affected countries in south-eastern Europe, such as Bulgaria and Romania, where there was no evidence of ASF spread to other EU MS within one year.

Drivers for Livestock-Associated Methicillin-Resistant Staphylococcus Aureus Spread Among Danish Pig Herds - A Simulation Study.

To gain insight into the rapid increase in the number of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA)-positive herds in Denmark, we developed an individual-based Monte Carlo simulation model. We aimed to assess whether transmission of LA-MRSA via pig movements could explain the observed increase in the number of positive herds in Denmark, and to evaluate the effect of other between-herd transmission mechanisms. Pig movements alone were not sufficient to mimic the observed increase in LA-MRSA-positive herds in Denmark in any of the modelled scenarios. The model identified three factors that played important roles in the between-herd spread of LA-MRSA: (1) the within-herd dynamics, (2) the frequency and effectiveness of indirect transmissions, and (3) unexplainable introduction of LA-MRSA to swine herds. These factors can act as starting points for the development of LA-MRSA control programs in pig herds in order to limit the risk of its transmission to humans.

Building the foundation for veterinary register-based epidemiology: A systematic approach to data quality assessment and validation.

Epidemiological studies often use data from registers. Data quality is of vital importance for the quality of the research. The aim of this study was to suggest a structured workflow to assess the quality of veterinary national registers. As an example of how to use the workflow, the quality of the following three registers was assessed: the Central Husbandry Register (CHR), the database for movement of pigs (DMP) and the national Danish register of drugs for veterinary use (VetStat). A systematic quantitative assessment was performed, with calculation the proportion of farms and observations with "poor quality" of data. "Poor" quality was defined for each measure (variable) either as a mismatch between and/or within registers, registrations of numbers outside the expected range, or unbalanced in- and outgoing movements. Interviews were conducted to make a complementary qualitative assessment. The proportion of farms and observations within each quality measure varied. This study highlights the importance of systematic quality assessment of register data and suggests a systematic approach for such assessments and validations without the use of primary data.

Simulating the epidemiological and economic effects of an African swine fever epidemic in industrialized swine populations.

African swine fever (ASF) is a notifiable infectious disease with a considerable impact on animal health and is currently one of the most important emerging diseases of domestic pigs. ASF was introduced into Georgia in 2007 and subsequently spread to the Russian Federation and several Eastern European countries. Consequently, there is a non-negligible risk of ASF spread towards Western Europe. Therefore it is important to develop tools to improve our understanding of the spread and control of ASF for contingency planning. A stochastic and dynamic spatial spread model (DTU-DADS) was adjusted to simulate the spread of ASF virus between domestic swine herds exemplified by the Danish swine population. ASF was simulated to spread via animal movement, low- or medium-risk contacts and local spread. Each epidemic was initiated in a randomly selected herd - either in a nucleus herd, a sow herd, a randomly selected herd or in multiple herds simultaneously. A sensitivity analysis was conducted on input parameters. Given the inputs and assumptions of the model, epidemics of ASF in Denmark are predicted to be small, affecting about 14 herds in the worst-case scenario. The duration of an epidemic is predicted to vary from 1 to 76days. Substantial economic damages are predicted, with median direct costs and export losses of €12 and €349 million, respectively, when epidemics were initiated in multiple herds. Each infectious herd resulted in 0 to 2 new infected herds varying from 0 to 5 new infected herds, depending on the index herd type.

The costs of preventive activities for exotic contagious diseases-A Danish case study of foot and mouth disease and swine fever.

The present paper provides an overview of the costs of preventive activities, currently undertaken in Denmark, related to foot and mouth disease (FMD) and classical and African swine fever (SF). Only costs held between outbreaks were included. Costs were divided into public costs and costs paid by the pig and cattle industries, respectively. Data were retrieved from multiple sources such as databases, legal documents, official statistics, yearly reports and expert opinions. As no previous studies have assessed such costs, data collection and estimation procedures were discussed and decided upon in a group of experts from universities, industry, and public authorities. The costs of each preventive activity were related to the type of activity, the number of times the activity was carried out and the share of costs that could be associated with FMD or SF. Uncertainty about parameters was incorporated in the analysis by assuming that the FMD/SF shares of costs as well as total costs for each activity could take on a most likely as well as a minimum and maximum value. A high degree of transparency was prioritized in the cost analysis, which enables reproducibility and easy access to conducting sensitivity analyses. A total of 27 FMD/SF preventive activities were identified. The estimated median (minimum-maximum) of total costs amounted to €32 (18-50) million in 2013. The single most costly FMD/SF related activity, amounting to €8 (5-13) million or 26% of total costs, was a national legal requirement to clean lorries immediately after transportation of live animals. The distribution of costs between stakeholders was estimated to be as follows: pig industry 63%, cattle industry 27%, and the public authorities 10%. Most of the activities focused on reducing the probability of spreading FMD/SF, while only a few activities were directed mainly towards reducing the probability of introduction. Legally required FMD/SF activities (mainly based on EU legislation) accounted for 60% of the activities, while FMD/SF related measures agreed on at sector level and measures implemented due to individual initiatives, such as farmer's investment in specially built delivery facilities, each accounted for 20%.

The impact of resources for clinical surveillance on the control of a hypothetical foot-and-mouth disease epidemic in Denmark.

The objectives of this study were to assess whether current surveillance capacity is sufficient to fulfill EU and Danish regulations to control a hypothetical foot-and-mouth disease (FMD) epidemic in Denmark, and whether enlarging the protection and/or surveillance zones could minimize economic losses. The stochastic spatial simulation model DTU-DADS was further developed to simulate clinical surveillance of herds within the protection and surveillance zones and used to model spread of FMD between herds. A queuing system was included in the model, and based on daily surveillance capacity, which was 450 herds per day, it was decided whether herds appointed for surveillance would be surveyed on the current day or added to the queue. The model was run with a basic scenario representing the EU and Danish regulations, which includes a 3 km protection and 10 km surveillance zone around detected herds. In alternative scenarios, the protection zone was enlarged to 5 km, the surveillance zone was enlarged to 15 or 20 km, or a combined enlargement of the protection and surveillance zones was modelled. Sensitivity analysis included changing surveillance capacity to 200, 350 or 600 herds per day, frequency of repeated visits for herds in overlapping surveillance zones from every 14 days to every 7, 21 and 30 days, and the size of the zones combined with a surveillance capacity increased to 600 herds per day. The results showed that the default surveillance capacity is sufficient to survey herds on time. Extra resources for surveillance did not improve the situation, but fewer resources could result in larger epidemics and costs. Enlarging the protection zone was a better strategy than the basic scenario. Despite that enlarging the surveillance zone might result in shorter epidemic duration, and lower number of affected herds, it resulted frequently in larger economic losses.

Quantitative assessment of the risk of introduction of bovine viral diarrhea virus in Danish dairy herds.

A quantitative risk assessment was carried out to estimate the likelihood of introducing bovine viral diarrhea virus (BVDV) in Danish dairy herds per year and per trimester, respectively. The present study gives important information on the impact of risk mitigation measures and sources of uncertainty due to lack of data. As suggested in the Agreement on the Application of Sanitary and Phytosanitary Measures (SPS Agreement), the OIE Terrestrial Animal Health Code was followed for a transparent science-based risk assessment. Data from 2010 on imports of live cattle, semen, and embryos, exports of live cattle, as well as use of vaccines were analyzed. Information regarding the application of biosecurity measures, by veterinarians and hoof trimmers practicing in Denmark and in other countries, was obtained by contacting several stakeholders, public institutions and experts. Stochastic scenario trees were made to evaluate the importance of the various BVDV introduction routes. With the current surveillance system, the risk of BVDV introduction was estimated to one or more introductions within a median of nine years (3-59). However, if all imported animals were tested and hoof trimmers always disinfected the tools used abroad, the risk could be reduced to one or more introductions within 33 years (8-200). Results of this study can be used to improve measures of BVD surveillance and prophylaxis in Danish dairy herds.