Whole genome analysis of a novel picornavirus related to the Enterovirus/Sapelovirus supergroup from porcine feces in Japan

•A novel picornavirus, SPPVJ, was identified in pig feces by using a metagenomics approach.•SPPVJ was organized like a standard picornavirus genome with a type IV IRES.•SPPVJ was related to bat picornaviruses isolated from bat feces in China.•SPPVJ were detected in 17.8% (19/107) of the feces from pigs in Japan. A novel virus related to the Enterovirus/Sapelovirus supergroup in the family Picornaviridae was identified in healthy porcine feces in Japan by using a metagenomics approach. The genome of the virus, named Sapelo-like porcine picornavirus Japan (SPPVJ) Pig/Isi-Im1/JPN/2016, had a type-IV internal ribosomal entry site and carried a 6978-nucleotide-long single open reading frame encoding a 2326 amino acids (aa) polyprotein precursor. The coding sequence region consisted of leader protein (68 aa), a structural protein region P1 (824 aa), and the non-structural protein regions P2 (672 aa) and P3 (762 aa). Among representative picornaviruses, the P1, 2C, and 3CD regions of SPPVJ had the highest aa identities of 64.4%, 61.9%, and 73.3%, respectively, with the corresponding regions of sapelo-like bat picornavirus BtVs-PicoV/SC2013. Sequencing analysis of the RT-PCR products derived from the 5' untranslated and 3D regions revealed the presence of SPPVJ in 17.8% (19/107) of the feces from healthy and diarrheal pigs in 12 farms in 2015–2016. Further studies are needed to determine the origin and pathogenic potential of SPPJV in pigs and other mammals.