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.