Full-length genome of a novel genotype 3 hepatitis E virus strain obtained from domestic pigs in Japan

Abstract

Hepatitis E virus (HEV) causes acute or chronic hepatitis in humans and can be transmitted via the fecal-oral route. Pigs are one of the main reservoirs for this infection. Sixty pigs, 4-5 months of age, on a swine herd in Japan had detectable anti-HEV IgG antibodies, and five (8.3%) of them had ongoing infection of genotype 3 HEV. Five HEV strains obtained from the viremic pigs shared 98.8-100% nucleotide identity, and one representative strain (swHE1606845), whose entire genomic sequence was determined in this study, differed by 14.1-19.6% from the reported HEV strains of subtypes 3a-3k and by 14.7-19.1% from other genotype 3 HEV strains whose subtypes have not yet been assigned. swHE1606845 showed a higher nucleotide p-distance value of ≥0.143 with the genotype 3 HEV strains of subtypes 3a-3k and ≥0.152 with other genotype 3 strains of unassigned subtypes. A SimPlot analysis revealed a lack of recombination events. These results indicate that swHE1606845 is a candidate member of a novel subtype of genotype 3. Further efforts to identify the swHE1606845-like novel strain are warranted to clarify the origin of this strain and to determine the complete nucleotide sequences of two additional swHE1606845-like strains for assigning a new subtype.

Keywords: Complete genome; Domestic pigs; Hepatitis E virus; Novel subtype; Phylogenetic analysis.