The prevalence of hepatitis E virus in piglets on Czech pig production farms and phylogenetic analysis of recovered isolates

The aim of our study was to determine the prevalence of hepatitis E virus (HEV) in domestic pigs and to investigate the genetic divergence of swine HEV in the Czech Republic. To this end, a one-step real time RT-PCR assay was introduced as a screening method while nested RT-PCR was used as an additional method to obtain specific sequences from the HEV genome and thus to perform sequence analysis. A total of 63 piglets originating from 14 farms were examined. Bile and intestinal contents were collected from each animal. At least one HEV RNA positive piglet was found in ten (71.4%) of the monitored farms. HEV RNA was most frequently detected in bile samples (34.9%) compared to intestinal content samples (22.2%). In nine piglets (14.3%), both biological samples were HEV RNA-positive. Based on these results sequence and phylogenetic analysis of one randomly selected HEV isolate originating from each HEV RNA-positive farm was performed. Analysis of 287 bp PCR products of the ORF1 gene showed that all the studied HEV isolates could be classified into genotype 3 and subgenotypes 3f and 3g. The failure to find any 100% homology between our isolates and HEV isolates deposited in the GenBank confirms the significant variability within the HEV genome.