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Hepatitis E virus (HEV) is the causative agent of hepatitis E — an emerging zoonotic disease distributed worldwide. The aim of this study was to determine the prevalence of HEV in Slovakian domestic pigs, as this has not been studied yet. Clinical samples (n = 269) from fourteen randomly selected domestic pig farms for three different age categories of pigs were analysed and the subsequently detected isolates were genetically characterized. The reverse transcriptase polymerase chain reaction (RT-PCR) analysis revealed that 32 pigs (11.9 %) of all age categories were HEV RNA positive. The highest occurrence was detected in fattening pigs (14.8 %) and the lowest in weaning pigs (12.5 %). The HEV RNA was not observed at all in the youngest category (the suckling piglets). The phylogenetic analysis revealed that all Slovak HEV isolates clustered into two genetic groups of the genotype HEV-3.

Hepatitis E virus (HEV) represents the causative agent of acute viral hepatitis in the world. The virus belongs to the genus Paslahepevirus, species Paslahepevirus balayani, which contains 8 different genotypes and at least 14 reference HEV-3 subtypes. Recently we have identified three isolates in a Slovakian pig farm as a new unclassified HEV-3 subtype. The aim of this study was to sequence and analyze additional regions of HEV genome for PER5 isolate, a representative isolate of potential new HEV-3 subtype. The phylogenetic analyses of 749 bp and 828 bp DNA fragments amplified from ORF1 revealed that both sequences fall outside two major clades (3abchij and 3efg) of the HEV-3 genotype as well as the other HEV-3 subtypes. The nucleotide identity with other HEV-3 subtypes indicated low values within the range 79.2–84.1 % as well. The results provide further support for the circulation of a new HEV-3 subtype in the pig farm in Slovakia.

The COST action "Standardising output-based surveillance to control non-regulated diseases of cattle in the European Union (SOUND control)," aims to harmonise the results of surveillance and control programmes (CPs) for non-EU regulated cattle diseases to facilitate safe trade and improve overall control of cattle infectious diseases. In this paper we aimed to provide an overview on the diversity of control for these diseases in Europe. A non-EU regulated cattle disease was defined as an infectious disease of cattle with no or limited control at EU level, which is not included in the European Union Animal health law Categories A or B under Commission Implementing Regulation (EU) 2020/2002. A CP was defined as surveillance and/or intervention strategies designed to lower the incidence, prevalence, mortality or prove freedom from a specific disease in a region or country. Passive surveillance, and active surveillance of breeding bulls under Council Directive 88/407/EEC were not considered as CPs. A questionnaire was designed to obtain country-specific information about CPs for each disease. Animal health experts from 33 European countries completed the questionnaire. Overall, there are 23 diseases for which a CP exists in one or more of the countries studied. The diseases for which CPs exist in the highest number of countries are enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis, bovine viral diarrhoea and anthrax (CPs reported by between 16 and 31 countries). Every participating country has on average, 6 CPs (min-max: 1-13) in place. Most programmes are implemented at a national level (86%) and are applied to both dairy and non-dairy cattle (75%). Approximately one-third of the CPs are voluntary, and the funding structure is divided between government and private resources. Countries that have eradicated diseases like enzootic bovine leukosis, bluetongue, infectious bovine rhinotracheitis and bovine viral diarrhoea have implemented CPs for other diseases to further improve the health status of cattle in their country. The control of non-EU regulated cattle diseases is very heterogenous in Europe. Therefore, the standardising of the outputs of these programmes to enable comparison represents a challenge., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Hodnik, Acinger-Rogić, Alishani, Autio, Balseiro, Berezowski, Carmo, Chaligiannis, Conrady, Costa, Cvetkovikj, Davidov, Dispas, Djadjovski, Duarte, Faverjon, Fourichon, Frössling, Gerilovych, Gethmann, Gomes, Graham, Guelbenzu, Gunn, Henry, Hopp, Houe, Irimia, Ježek, Juste, Kalaitzakis, Kaler, Kaplan, Kostoulas, Kovalenko, Kneževič, Knific, Koleci, Madouasse, Malakauskas, Mandelik, Meletis, Mincu, Mõtus, Muñoz-Gómez, Niculae, Nikitović, Ocepek, Tangen-Opsal, Ózsvári, Papadopoulos, Papadopoulos, Pelkonen, Polak, Pozzato, Rapaliuté, Ribbens, Niza-Ribeiro, Roch, Rosenbaum Nielsen, Saez, Nielsen, van Schaik, Schwan, Sekovska, Starič, Strain, Šatran, Šerić-Haračić, Tamminen, Thulke, Toplak, Tuunainen, Verner, Vilček, Yildiz and Santman-Berends.)

Some European countries have successfully implemented country-specific control programs (CPs) for infectious cattle diseases that are not regulated or are regulated only to a limited extent at the European Union (EU) level. Examples of such diseases include bovine viral diarrhea (BVD), infectious bovine rhinotracheitis (IBR), and Johne's disease (JD). The CPs vary between countries in the design and quality of collected data as well as methods used to detect infection and estimate prevalence or probability of freedom from infection. Differences in disease status between countries and non-standardized approaches to assess freedom from infection pose a risk for countries with CPs for non-regulated diseases as infected animals may influence the progress of the disease control or eradication program. The implementation of output-based standards allows estimation and comparison of the probability of freedom for non-regulated cattle diseases in European countries. The aim of the current study was to assess the existence and quality of data that could be used for estimating freedom from infection in European countries. The online data collection tool was sent to 32 countries participating in the SOUND control COST Action and was completed by 24 countries. Data on cattle demographics and data from CPs of IBR and BVD exist in more than 50% of the response countries. However, data describing risk factors and CP of JD was reported as existing in <25% of the countries. The overall quality of data in the sections on demographics and CPs of IBR and BVD were evaluated as "good", but risk factors and JD data were mostly evaluated as "fair." Data quality was considered less good mainly due to two quality criteria: accessibility and accuracy. The results of this study show that the quantity and quality of data about cattle populations and CPs are relatively similar in many surveyed countries. The outcome of this work provides an overview of the current situation in the European countries regarding data on EU non-regulated cattle diseases and will further assist in the development and implementation of output-based standards., Competing Interests: CFa was employed by the company Ausvet Europe. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Rapaliute, van Roon, van Schaik, Santman-Berends, Koleci, Mincu, Gethmann, Conrady, Knific, Hodnik, Berezowski, Carmo, Madouasse, Tarpai, Gerilovych, Malakauskas, Sekovska, Fourichon, Kalaitzakis, Roch, Houe, Dudek, Mõtus, Ózsvári, Costa, Guelbenzu-Gonzalo, Henry, Alishani, Pozzato, Hopp, Juste, Strain, Mandelik, Vilček, Autio, Tamminen and Faverjon.)

Background: Hepatitis E virus (HEV) is agent causing hepatitis worldwide. Originally considered to be limited to developing countries, this virus was also detected in developed countries. In recent years an increasing number of reports indicate that farmed domestic pigs are widely infected with HEV in several European countries. The HEV status in Slovakia is still missing., Results: In this study, the circulation of HEV among domestic swine in Slovakia and genetic diversity of the virus was studied. Overall HEV RNA was detected in 53/388 (13.7, 95% CI: 10.40-17.48%) pig rectal swabs in five production stages (age categories) with statistically significant differences among all the stages. The highest HEV prevalence was observed in weaners 24/81 (29.6, 95% CI: 19.99-40.81%) and then significantly declined in growers and fatteners. No HEV was detected in suckling piglets and sows. Twenty-eight partial sequences of ORF1 (242 bp) and seventeen of ORF2 (304 bp) were analysed. Phylogenetic analysis and p-distance comparisons confirmed in both ORFs that all Slovak HEV sequences belong to the genotype HEV-3, major clade 3abchij with higher identity to 3a and 3i subtypes. Three sequences were outside of all lastly updated HEV-3 subtypes., Conclusion: This is the first report to fill the information gap about HEV infection in pigs in Slovakia. The results suggested a lower prevalence of HEV in Slovak pig farms than observed in other European countries. While most HEV isolates were typed as HEV-3 clade 3abchij, three sequences were unclassified.

As for other European countries, IBR is a significant cause of financial losses in cattle in Slovakia. The State Veterinary and Food Administration of the Slovak Republic prepared a voluntary IBR control program for cattle farms in 1995, which was implemented in 1996. In subsequent years, 48-119 farms/year enrolled in the voluntary IBR control program. Since the end of 2006, the IBR control program became compulsory by law for all cattle farms in Slovakia. Serology was used to identify infected animals using a conventional ELISA amongst non-vaccinated cattle and a gE specific ELISA in cattle vaccinated with marker vaccine. Eradication is based on culling when the serological prevalence of IBR in a herd is below 15%. When the prevalence is higher than 15%, the culling is combined with the application of a marker vaccine. A radical method where all animals are slaughtered is used with the agreement of the farmer when appropriate, especially for very small herds. Depending upon the selected eradication method, the antibody positive cattle can be gradually replaced in the herds to eliminate financial losses due to the disease. The movement of cattle is under strict control requiring a health certificate issued by the state veterinary authority and the movement must be recorded in the central livestock registry. The next step for herds is monitoring to achieve official IBR-free status. Based on the official figures from The State Veterinary and Food Administration, 60.2% herds were free of IBR in Slovakia in 2020., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Mandelik, Bires, Ozsvari, Hodnik and Vilcek.)

Background: Surveillance and characterization of pig enteric viruses such as transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), rotavirus, astrovirus (PAstV), sapovirus (PSaV), kobuvirus and other agents is essential to evaluate the risks to animal health and determination of economic impacts on pig farming. This study reports the detection and genetic characterization of PAstV, PSaV in healthy and diarrheic domestic pigs and PEDV and TGEV in diarrheic pigs of different age groups., Results: The presence of PAstV and PSaV was studied in 411 rectal swabs collected from healthy (n = 251) and diarrheic (n = 160) pigs of different age categories: suckling (n = 143), weaned (n = 147) and fattening (n = 121) animals on farms in Slovakia. The presence of TGEV and PEDV was investigated in the diarrheic pigs (n = 160). A high presence of PAstV infections was detected in both healthy (94.4%) and diarrheic (91.3%) pigs. PSaV was detected less often, but also equally in clinically healthy (8.4%) and diarrheic (10%) pigs. Neither TGEV nor PEDV was detected in any diarrheic sample. The phylogenetic analysis of a part of the RdRp region revealed the presence of all five lineages of PAstV in Slovakia (PAstV-1 - PAstV-5), with the most frequent lineages being PAstV-2 and PAstV-4. Analysis of partial capsid genome sequences of the PSaVs indicated that virus strains belonged to genogroup GIII. Most of the PSaV sequences from Slovakia clustered with sequences originating from neighbouring countries., Conclusions: Due to no significant difference between healthy and diarrheic pigs testing of the presence of PAstV and PSaV provides no diagnostic value. Genetic diversity of PAstV was very high as all five lineages were identified in pig farms in Slovakia. PSaV strains were genetically related to the strains circulating in Central European region.

This report describes the first disease outbreak caused by chimeric swine enteric coronavirus (SeCoV) on two pig farms in Slovakia in early 2015. The infection was introduced by import of two breeding boars which were placed in provisional quarantine in a unit not strictly separated from other healthy pigs in the same building. Subsequently, loss of appetite and diarrhoea were observed in both boars during the first three days in the isolation unit. The infection gradually spread to the farrowing area and throughout the farm in two weeks and later to another nearby farm. Yellow watery diarrhoea accompanied by dehydration and death was observed in piglets with a mortality ranging from 30 to 35%. In the absence of an available vaccine, the pregnant sows were dosed by mouth with a 10% suspension prepared from the intestine and faeces of infected piglets in warm water. Three weeks after dosing, new litters of piglets were born which remained healthy with no development of diarrhoea.

The porcine kobuvirus 1 (PKV-1) is believed to be an enteric virus. To investigate the prevalence of PKV-1 in pigs, virus was detected by RT-PCR in rectal swabs originating from 414 healthy and diarrheic pigs of different age categories on farms in Slovakia. Among all ages of animals, PKV-1 was detected equally in diarrheic (63.8%) and clinically healthy (62.9%) pigs. PKV-1 was more often detected in diarrheic (74.6%) than in healthy (64.4%) suckling piglets (<28days) but data was not statistically significant. Results in weaned (28-70days) and fattening (>70days) of both healthy and diarrheic pigs were inconsistent ranging in interval 56.2% to 67.9%. This study did not confirm a clear relationship of PKV-1 infection with diarrhea in pigs. Rotavirus A infection was detected among the same animals in 39% diarrheic and 9.2% healthy suckling piglets (p<0.001) confirming rotavirus as a causative agent of diarrhea in this age group. The difference was not significant in older pigs with both diarrheic and healthy pigs being infected within a range of 0% to 12.2%. Co-infection with PKV-1 and rotavirus A was detected overall in 5.6% of healthy and in 13.5% of diarrheic pigs and was highest in suckling piglets (33.9%). The PKV-1sequences from pigs in Slovakia were analyzed at the genetic level in the partial 3D gene region for the first time. The viral sequences were grouped in phylogenetic clusters according to their farm of origin. When compared with 157 nucleotide sequences originating from pig samples of different countries around the world Slovakian PKV-1 sequences were clustered in the phylogenetic tree with Asian sequences but not with nucleotide sequences from the neighbouring countries of Czech Republic or Hungary., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)