Proposal for a new subtype of the zoonotic genotype 3 Hepatitis E virus: HEV-3l

•The nearly complete genomes of two Italian porcine hepatitis E strains were sequenced.•The HEV strains detected were related each other and with a France swine strain.•These strains were classified in a novel subtype named HEV-3l. The near-complete genomic sequences of two hepatitis E virus (HEV) strains, detected from feces of infected pigs, were obtained. Phylogenetic analysis and p-distance comparisons of the complete coding regions showed a close relationship to the French swine strain FR-SHEV3c-like detected in 2006 (p-distance value 0.101), belonging to HEV-3 but not assigned to any known subtype. The three HEV sequences showed, relatively high nucleotide distances (p-distance >0.129) compared to the other defined HEV subtype references and unclassified strains. The HEV classification criteria and the high sequence similarity suggest that these strains can be assigned to a putative novel subtype of genotype 3, HEV-3l.