Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age.

The porcine enteric virome comprises a wide range of eukaryotic and prokaryotic viruses in healthy and diarrheic pigs. As RNA viruses are considered to be important agents responsible for diarrhoea in pigs, this work was focused on the RNA virome. To identify viruses, a next generation sequencing technique and bioinformatics analysis was employed. A wide spectrum of viral genera with RNA genomes, such as Kobuvirus, Picobirnavirus, Teschovirus, Posavirus, Mamastovirus, Enterovirus and Rotavirus were identified in both diarrheic and healthy pigs. No clear differences in the virome composition were found between healthy and diarrheic pigs. The data visualisation using Non-Metric Multidimensional Scaling as well as by the Analysis of Similarities test suggested that the virome depended on the age of animals and differed in piglets when compared to weaned and fattening pigs.

The role of molecular-genetic techniques in BVDV eradication in Lower Austria.

A voluntary bovine viral diarrhoea virus (BVDV) control programme, which later became a compulsory eradication programme, based on the Swedish model was introduced in Lower Austria in 1997. The persistently infected animals were detected by Ag-ELISA and all samples were re-tested by the improved single-tube RT-PCR, employing panpestivirus primers targeting the 5'-UTR of the virus genome. In 2010, the BVDV eradication programme, which became compulsory from 2004, reached the final stage with only five remaining infected herds in which BVDV was difficult to eradicate. To resolve the problem in those herds, a molecular epidemiology approach was used. No differences in the spectrum of BVDV-1 subgenotypes at the beginning and at the final stage of eradication programme were found. The genetic study revealed the importance of human risk factor when finishing an eradication programme. Molecular epidemiology was also used to analyse BVDV isolates associated with re-introductions to BVDV-free herds.

Existence and Quality of Data on Control Programs for EU Non-regulated Cattle Diseases: Consequences for Estimation and Comparison of the Probability of Freedom From Infection.

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.

Identification and genetic diversity of hepatitis E virus in domestic swine from Slovakia.

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.

Infectious Bovine Rhinotracheitis Control Program in Slovakia.

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.

Innovative Animal Model of DSS-Induced Ulcerative Colitis in Pseudo Germ-Free Mice.

The aim of this study was to investigate the use of a standardized animal model subjected to antibiotic treatment, and the effects of this treatment on the course of dextran sodium sulphate (DSS)-induced colitis in mice. By decontamination with selective antibiotics and observation of pathogenesis of ulcerative colitis (UC) induced chemically by exposure of mice to various concentrations of DSS, we obtained an optimum animal PGF model of acute UC manifested by mucin depletion, epithelial degeneration and necrosis, leading to the disappearance of epithelial cells, infiltration of lamina propria and submucosa with neutrophils, cryptitis, and accompanied by decreased viability of intestinal microbiota, loss of body weight, dehydration, moderate rectal bleeding, and a decrease in the selected markers of cellular proliferation and apoptosis. The obtained PGF model did not exhibit changes that could contribute to inflammation by means of alteration of the metabolic status and the induced dysbiosis did not serve as a bearer of pathogenic microorganisms participating in development of ulcerative colitis. The inflammatory process was induced particularly by exposure to DSS and its toxic action on compactness and integrity of mucosal barrier in the large intestine. This offers new possibilities of the use of this animal model in studies with or without participation of pathogenic microbiota in IBD pathogenesis.

The Influence of Feed-Supplementation with Probiotic Strain Lactobacillus reuteri CCM 8617 and Alginite on Intestinal Microenvironment of SPF Mice Infected with Salmonella Typhimurium CCM 7205.

Alginite is a non-ore raw material arising by fossilization of accumulated organic (algae) and inorganic material, particularly clay, carbonates, quartz, and amorphous modification of silicic acid in the aqueous environment. Humic acids as a component of organic portion of alginite are known for very good buffering ability which allows them to stabilise pH throughout the digestion system of animals, stimulate receptors of the immune system in intestinal villi against pathogenic bacteria, and support proliferation and activity of beneficial bacteria (lactobacilli, bifidobacteria, and similar). Our investigations focused on the influence of a probiotic strain in combination with alginite on intestinal microenvironment of SPF mice infected with Salmonella Typhimurium. The 66 female mice (BALB/c) used in our study were divided to four experimental groups, control NC1, control NC2 (alginite), IC (alginite + Salmonella Typhimurium CCM 7205NAL), LAB (Lact. reuteri CCM 8617 + alginite + Salm. Typhimurium CCM 7205NAL). The group supplemented with Lact.reuteri CCM 8617 and alginite showed significant reduction in growth of Salm. Typhimurium in mice faeces at 24 and 72 h (P < 0.001) post infection. The supplementation of additives affected positively also nitrogen, enzymatic, hepatic and energy metabolism of mice. The demonstrable positive influence of additives alleviated the negative impact of Salm. Typhimurium infection on the morphology investigated in the jejunum and ileum of LAB group of mice. The livers of mice treated with both alginite and Lact.reuteri CCM 8617 showed marked reduction of overall inflammation, hepatocyte necrosis and size of typhoid nodules.

Genetic identification of astroviruses in wild boars.

Astroviruses are widely detected in pigs but their detection in wild boars is rather sporadic. In this study, astroviruses were detected in organ homogenates of wild boars by applying nested reverse transcriptase polymerase chain reaction, and the typing was carried out by phylogenetic analysis. Overall, 30/200 (15.0%) homogenates were positive for astroviruses. Genetic typing revealed that of 13 amplicons analyzed, 8 were typed as porcine astrovirus lineage 2 (PAstV-2), 2 as lineage 4 (PAstV-4), 2 identical sequences were grouped with chicken astrovirus, and 1 sequence belonged to a bat astrovirus lineage. This first identification of chicken and bat astroviruses in wild boars indicates interspecies transmission.

Molecular detection of enteric viruses and the genetic characterization of porcine astroviruses and sapoviruses in domestic pigs from Slovakian farms.

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.

First outbreak with chimeric swine enteric coronavirus (SeCoV) on pig farms in Slovakia - lessons to learn.

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.

Porcine kobuvirus 1 in healthy and diarrheic pigs: Genetic detection and characterization of virus and co-infection with rotavirus A.

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.

Identification and molecular characterization of border disease virus (BDV) from sheep in India.

Pestiviruses isolated from sheep and goats in India thus far have been bovine viral diarrhoea virus 1 (BVDV-1) or BVDV-2. During routine genetic typing of pestiviruses in the years 2009-10, border disease virus (BDV) was detected in eight Indian sheep of a flock showing clinical signs of BD by real time RT-PCR. All the samples yielded positive virus isolates in cell culture but were found negative by a BVDV antigen ELISA. A representative BDV isolate was characterized at genetic and antigenic level. Phylogenetic analysis carried out in 5'-UTR, N(pro) and E2 regions of genome typed the Indian BDV isolate as BDV-3. A more detailed analysis in N(pro) and entire region coding structural proteins showed that the N(pro) (168), C (100 aa), E(rns) (227 aa), E1 (195 aa) and E2 (373 aa) proteins were of size characteristic for BDV reference strain X818. Antigenic differences were evident between the BDV-3 isolate and previously reported BDV-1, BDV-5 and BDV-7 strains. Although origin of BDV-3 in India is not clear, the results reflect probable introduction through trade in sheep between India and other countries or BDV-3 may be more widely distributed. Additionally, this study suggests that for diagnosis of BDV infection, the commercial BVDV Ag-ELISA should be used with caution. This is the first identification of BDV in sheep in India which highlights the need for continued pestivirus surveillance and assessing its impact on sheep and goat production.

CHARACTERIZATION OF PORCINE PARVOVIRUS TYPE 3 AND PORCINE CIRCOVIRUS TYPE 2 IN WILD BOARS (SUS SCROFA) IN SLOVAKIA.

As the number of free-living wild boars (Sus scrofa L.) continues to rise in Slovakia, the probability of pathogen transmission between susceptible species increases. We investigated the distribution and genetic characterization of porcine parvovirus type 3 (PPV3), porcine circovirus type 2 (PCV2), and their coinfection in wild boars. Among 194 animals tested, 19.1% were positive for PPV3 and 43.8% for PCV2. Similar rates of coinfection with both viruses reaching 11.0% and 11.8% were observed in juvenile and mature wild boars, respectively. Phylogenetic analysis of PPV3 sequences from VP1 and NS1 genomic regions revealed a close genetic relationship among isolates from Slovakia and those sampled worldwide. Prevalence of PCV2 in wild boars was lower than that reported in domestic pigs in Slovakia. The PCV2 variants originating from sylvatic and domestic hosts in Slovakia were grouped in the same clusters, namely PCV2b-1A/1B and PCV2a-2D.

The first detection of PRRSV in wild boars in Slovakia.

PRRSV was confirmed by a nested RT-PCR in two out of 129 samples originating from wild boars from Eastern Slovakia. Virus isolates were genetically typed in ORF7 as PRRSV-1, EU-1 with 99.7% (sample 14WB) and 100% (sample 10WB) nucleotide sequence similarity to Lelystad reference strain and Porcilis PRRS vaccine strain, respectively. The origin of PRRSV in these wild boars is unclear but it is highly likely that virus was transmitted from vaccinated domestic pigs to wild boars.

The presence of six potentially pathogenic viruses in pigs suffering from post-weaning multisystemic wasting syndrome.

BACKGROUND: Porcine circovirus type 2 (PCV2) is an etiological agent of porcine circovirus diseases (PCVDs). Post-weaning multisystemic wasting syndrome (PMWS) as the most important PCVD is considered a multifactorial disease. It was demonstrated that not only PCV2 but several viruses are associated with PMWS. Studies of viral co-infections in PMWS pigs led often to controversial results. The aim of this work was to determine the presence of emerging (PRRSV), re-emerging (PTV) and newly-emerging (TTSuV1, TTSuV2, PBoV1) viruses in samples of dead pigs suffering from PMWS. The impact of vaccination against PCV2 and the influence of age on the occurrence of single and multiple viral infections in pigs were also investigated. RESULTS: Viruses were detected by PCR, RT-PCR and real-time PCR in the pooled tissue samples (lymph nodes, liver and spleen) of pigs with PMWS (n = 56) which were divided into three groups: suckling piglets, post-weaning pigs and fattening pigs. In addition, lymph node samples were collected from apparently healthy fattening pigs (n = 59). The effect of vaccination against PCV2 with Ingelvac CircoFlex vaccine was also investigated. Between non-vaccinated pigs, the highest prevalence of individual viruses and multiple viral infections were found in diseased post-weaning and fattening animals with PMWS. Severe clinical disease was observed in swine co-infected with PCV2 and PRRSV. The prevalence of TTSuV1 and TTSuV2 was high in all groups of pigs and did not appear to have a significant effect on the syndrome. Simultaneous infection with TTSuV1 and PBoV1 was frequently confirmed in pigs with PMWS. No healthy pig was found to be infected with PRRSV, PTV or PBoV1. Vaccination against PCV2 did not influence the prevalence of TTSuVs, but significantly protected pigs against multiple viral infections. CONCLUSIONS: Post-weaning PMWS pigs were more often co-infected with viral pathogens than suckling or fattening pigs. Co-infection with PRRSV enforces clinical signs of PMWS, the influence of other viral co-infections is not clear. Vaccination against PCV2 significantly reduced viral co-infections in pigs.

Molecular characterization of border disease virus strain Aveyron.

For the pestivirus border disease virus (BDV) at least seven major genotypes have been described (BDV-1-BDV-7). So far, complete genomic sequences have been reported for four BDV genotypes (BDV-1-BDV-4). In this study we report the entire genomic sequence of the noncytopathogenic (ncp) BDV-5 reference strain Aveyron. The viral genome encompasses 12,284 nucleotides (nt) and contains one large open reading frame (11,700 nt) flanked by a 370 nt long 5'-untranslated region (UTR) and a 214 nt long 3'-UTR. The genome organization as well as the lengths of the viral polyprotein (3899 amino acids) and the 5'-UTR are very similar to the ones of other BDV strains, while the 3'-UTR of BDV Aveyron is considerably shorter when compared to other BDV strains. Comparative analysis of complete coding sequences revealed that BDV Aveyron shares nucleotide sequence identities of 76.9% to 79.0% with the other BDV strains, and less than 72% identity with other pestiviruses. In contrast to other BDV strains, a unique insertion of four amino acids (KAPD) of unknown origin is present in the C-terminal part of the viral autoprotease NS2 encoded by BDV Aveyron. Immunoblot analysis revealed that infection of cells with the ncp BDV strain Aveyron comprising this unique insertion in NS2 resulted in the expression of high amounts of NS3 and thereby showed that BDV Aveyron significantly differs from other ncp BDV strains in terms of NS2-3 processing and production of NS3.

Analysis of BVDV isolates and factors contributing to virus transmission in the final stage of a BVDV eradication program in lower Austria.

The BVDV eradication program in Lower Austria according to the Swedish model started in 1997 as a voluntary strategy and became obligatory for all herd owners in 2004. In this paper we analyse BVDV isolates found in PI animals of the last infected cattle farms at the genetic level and describe possible risk factors for virus transmission in the final stage of the BVDV eradication program in Lower Austria, where only five infected herds were identified in 2010. Viral isolates from 23 farms on which PI animals had been detected in 2009 (n = 10), 2010 (n = 5), 2008 (n = 5) and in 2006 (n = 3) were analysed at a genetic level at the 5'-UTR. All isolates analysed by phylogenetic analysis fall into five BVDV-1 subgenotypes, i.e., b, e, f, g, and h. No new subgenotypes were identified when compared to isolates analysed at the beginning of the BVDV eradication program. The phylogenetic analysis also revealed three groups of herds with genetically identical isolates; the first group comprised two herds, the second seven herds and the third four herds. Analysis of several factors such as distance between herds, purchase of cattle, work of farmers, veterinarians, assistants of milk recording associations and animal carriers indicated the latter as the most critical factor for transmitting the same viruses. Seven herds of two groups of identical BVDV isolates were served by the same cattle carrier, six herds shared the veterinarian and five herds had the same assistant of the milk recording association who could be the risk factor for the introduction of BVDV into the herd. The analysis helped to stop virus transmission. Therefore, from early 2012 up to now, no new infection has occurred in Lower Austria. The results indicated that biosecurity is a very important factor to prevent the spreading of viruses in the final stage of the BVDV eradication program.

Identification of a new unusual length polymorphism of the nucleocapsid protein in porcine reproductive and respiratory syndrome virus.

All twenty-nine PRRSV ORF7 nucleotide sequences obtained from clinical samples originating from the three Central European countries Austria (n = 7), Czech Republic (n = 12), and Slovakia (n = 10) belonged to type 1, subtype I (EU-1). Twenty-seven sequences encoded the typical length of the nucleocapsid protein composed of 128 amino acids. Two genetically identical ORF7s of PRRSV originating from a single farm in Slovakia showed a new length polymorphism of the nucleocapsid protein comprising 132 amino acids.

Development of a Plexor real-time PCR assay for the detection of porcine circovirus type 2.

A novel, real-time PCR system for the detection of porcine circovirus type 2 (PCV2) was developed. The system employed Plexor technology and detected 10(8)-10(1) copies per reaction of PCV2 DNA within a recombinant plasmid. The examination of clinical material showed consistent diagnostic sensitivity when samples contained more than 10(3) viral copies per reaction. Specificity of Plexor real-time PCR was confirmed using the porcine viruses PCV1, PRRSV, CSFV, TTSuV1 and TTSuV2 employing the melting curve analysis of PCR products. The low values of coefficient of variation in the intra- (1.74%) and inter-assay (2.41%) analysis suggested that the assay was a highly reproducible. The Plexor real-time PCR was compared with three other real-time PCR systems (SYBR Green, TaqMan, LUX) with conclusion that it can be used as a method of choice for the detection and quantitation of PCV2.

Phylogenetic analysis of recent classical swine fever virus (CSFV) isolates from Assam, India.

Classical swine fever (CSF), a highly contagious viral disease of pigs, is endemic in India. As there is no information concerning the accurate genetic typing of classical swine fever virus (CSFV) isolates in India, 16 CSF viruses isolated during 2005-2007 from domestic pigs in different districts of Assam were typed in 5' UTR (150 nucleotides). To confirm the genetic typing results and to study the genetic variability, selected viruses were also analyzed in E2 (190 nt) and NS5B gene (409 nt) regions. Phylogenetic analysis revealed that all the 16 CSFV isolates analyzed belonged to group 1 and subgroup 1.1 in contrast to the situation in other Asian countries. Additionally, analysis in E2 and NS5B region placed the Indian isolates in a clearly separated clade within subgroup 1.1. The results suggest that subgroup 1.1 CSF viruses are currently circulating in India, which is important for epidemiology and control of CSF.