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

•Five of 60 domestic pigs on a farm in Japan had HEV genomes (≥98.8% identity).•The complete genomic sequence of a swine HEV strain was determined.•No significant evidence of recombination was found.•The HEV strain differed from the reported genotype 3 HEV strains by ≥14.1%.•The HEV strain may belong to a novel subtype within the genotype 3 strain.