Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses

• Published in: Virus genes Vol. 55; no. 2; pp. 198 - 208
• Main Authors: Sunaga, Fujiko, Masuda, Tsuneyuki, Ito, Mika, Akagami, Masataka, Naoi, Yuki, Sano, Kaori, Katayama, Yukie, Omatsu, Tsutomu, Oba, Mami, Sakaguchi, Shoichi, Furuya, Tetsuya, Yamasato, Hiroshi, Ouchi, Yoshinao, Shirai, Junsuke, Mizutani, Tetsuya, Nagai, Makoto
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-04-2019; Springer Nature B.V
• Subjects: 3' Untranslated regions; Animals; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Breakpoints; Diarrhea - genetics; Diarrhea - veterinary; Diarrhea - virology; Feces - virology; Genetic diversity; Genetic Variation; Genome, Viral - genetics; Genomes; Genomic analysis; Genotypes; Insertion; Internal ribosome entry site; Medical Microbiology; Phylogenetics; Phylogeny; Picornaviridae - genetics; Picornaviridae - pathogenicity; Picornaviridae Infections - genetics; Picornaviridae Infections - veterinary; Picornaviridae Infections - virology; Plant Sciences; Recombination; Ribonucleic acid; RNA; Suidae; Swine - genetics; Swine - virology; Swine Diseases - genetics; Swine Diseases - virology; Virology; VP1 protein; Porcine feces; Complete genome analysis; Japan; Molecularly characterization; Sapelovirus A
• ISSN: 0920-8569; 1572-994X
• DOI: 10.1007/s11262-019-01640-8

The
Porcine Sapelovirus
(PSV) is an enteric virus of pigs that can cause various disorders. However, there are few reports that describe the molecular characteristics of the PSV genome. In this study, almost the entire genomes of 23 PSVs detected in Japanese pigs were analyzed using bioinformatics. Analysis of the
cis
-active RNA elements showed that the predicted secondary structures of the internal ribosome entry site in the 5′ untranslated region (UTR) and a
cis
-replication element in the 2C coding region were conserved among PSVs. In contrast, those at the 3′ UTR were different for different PSVs; however, tertiary structures between domains were conserved across all PSVs. Phylogenetic analysis of nucleotide sequences of the complete VP1 region showed that PSVs exhibited sequence diversity; however, they could not be grouped into genotypes due to the low bootstrap support of clusters. The insertion and/or deletion patterns in the C-terminal VP1 region were not related to the topology of the VP1 tree. The 3CD phylogenetic tree was topologically different from the VP1 tree, and PSVs from the same country were clustered independently. Recombination analysis revealed that recombination events were found upstream of the P2 region and some recombination breakpoints involved insertions and/or deletions in the C-terminal VP1 region. These findings demonstrate that PSVs show genetic diversity and frequent recombination events, particularly in the region upstream of the P2 region; however, PSVs could currently not be classified into genotypes and conserved genetic structural features of the
cis
-active RNA elements are observed across all PSVs.