Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses
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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.
KeywordsComplete genome analysis Japan Molecularly characterization Porcine feces Sapelovirus A
This work was supported by JSPS KAKENHI, via Grants 15K07718 and 18K05977.
FS, TM, MI, MA, YN, KS, YK, TO, MO, SS, TF, HY, YO, JS, TM, MN TM, and MN conceived of the study. FS, TF, JS, TM, and MN designed the study. TM, MI, MA, HY, and YO collected samples from pigs and carried out RT-PCR. YN, KS, YK, TO, MO, and SS analyzed data using bioinformatics. FS, KS, SS, TF, JS, TM, and MN wrote the paper. All authors approved the submitted manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
Research involving human participants and/or animals
This study did not involve any human participants and animals.
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