A Molecular Survey and Genetic Diversity of Hepatitis E Virus in Domestic Swine From Slovakia

Abstract 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 including neighbouring countries the Czech Republic and Hungary. 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%) pig rectal swabs in five production stages (age categories) with statistically highly significant differences (P < 0.01, χ2=28.444). No HEV was detected in suckling piglets and sows. The highest HEV incidence (29.6%) was observed in weaners and then declined in growers and fatteners. Twenty-eight partial sequences of ORF1 (242 bp) and seventeen of ORF2 (304 bp) were genetically 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 created a new branch, outside of major clades 3abchij and 3efg, showing high nucleotide p-distances (0.140-0.178). They could represent a novel subtype.Conclusion: This is the first report to fill the epidemiological gap about HEV infection in pigs in Slovakia. The results indicated a lower incidence of HEV in Slovak pig farms than observed in other European countries. While most HEV isolates were typed as HEV-3 clade3abchij, three sequences were most probably a candidate for a new HEV-3 subtype.