35Enterovirus G (EV-G) belongs to the family of Picornaviridae. Two types of recombinant porcine 36 EV-Gs carrying papain-like cysteine protease (PLCP) gene of porcine torovirus, a virus in 37 Coronaviridae, are reported. Type 1 recombinant EV-Gs are detected in pig feces in Japan, USA, 38 and Belgium and carry the PLPC gene at the junction site of 2C/3A genes, while PLPC gene 39 replaces the viral structural genes in type 2 recombinant EV-G detected in pig feces in a Chinese 40 farm. We identified a novel type 2 recombinant EV-G carrying the PLCP gene with flanking 41 sequences in place of the viral structural genes in pig feces in Japan. The ~0.3 kb-long upstream 42 flanking sequence had no sequence homology with any proteins deposited in GenBank, while the 43 downstream ~0.9 kb-long flanking sequence included a domain having high amino acid sequence 44 homology with a baculoviral inhibitor of apoptosis repeat superfamily. The pig feces, where the 45 novel type 2 recombinant EV-G was detected, also carried type 1 recombinant EV-G. Although the 46 phylogenetic analysis suggested that these two recombinant EV-Gs have independently evolved, 47 type 1 recombinant EV-G might have served as a helper virus by providing viral structural proteins 48 for dissemination of the type 2 recombinant EV-G. 49 50
Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.
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