Sequence Variation in Hepatitis E Virus Genotypes 3 and 4 from Swine Fecal Samples in Japan

Hepatitis E virus (HEV) is a causative agent for hepatitis. HEV is transmitted via the fecal-oral route through contaminated drinking water and induces zoonotic infections through eating uncooked and undercooked meat of deer, wild boar, and swine. In Japan, genotypes 3 (G3) and 4 (G4) are prevalent in domestic swine. Here, we examined the genetic variation among HEVs derived from swine fecal samples in Japan. A total of 320 samples were collected at 32 commercial farm facilities (1 fecal sample from each of 10 pig houses in individual farms). Viral RNA amplification at open reading frame (ORF) 3 was possible in 159 (49.7%) of the fecal samples. For genotyping, the same samples were subjected to amplification at ORF2 and the resulting amplicons were sequenced. The results revealed that all the HEVs in each farm belonged to the same cluster of G3 and G4: G3JP in 8 farms, G3SP in 4 farms, G3US in 6 farms, and G4JP in 2 farms, unclassified G3 in 2 farms, unable to decide due to a low rate of amplification in 5 farms, and no detection in 5 farms. Interestingly, the HEVs from one farm were more homogeneous than those of the same cluster that was derived from other farms. Thus, the efficiency of farm-to-farm transmission of HEVs is likely to be low and HEV seems to have evolved independently at each farm in Japan.