First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea

Abstract Enterovirus species G ( EV ‐G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV ‐G strain ( KOR / KNU ‐1811/2018) that resulted from cross‐order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV ‐G genome possessed an exogenous 594‐nucleotide (198‐amino acid) sequence, flanked by two viral 3C pro cleavage sites at the 5′ and 3′ ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain‐like cysteine protease ( PLCP ), which was recently found in the EV ‐G1, ‐G2, and ‐G17 genomes. The complete KNU ‐1811 genome shared 73.7% nucleotide identity with a prototype EV ‐G1 strain, but had 83.9%–86.7% sequence homology with the global EV ‐G1‐ PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV ‐G's own VP 1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1‐ PLCP and G17‐ PLCP strains respectively. These results implied that the torovirus‐derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV ‐G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV ‐G driven by infrequent viral recombination events, by which EV ‐G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.