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Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses

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Abstract

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.

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Acknowledgements

This work was supported by JSPS KAKENHI, via Grants 15K07718 and 18K05977.

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Authors and Affiliations

  1. School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan

    Fujiko Sunaga & Makoto Nagai

  2. Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan

    Tsuneyuki Masuda & Hiroshi Yamasato

  3. Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan

    Mika Ito

  4. Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki, 310-0002, Japan

    Masataka Akagami & Yoshinao Ouchi

  5. Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu, Tokyo, 183-8509, Japan

    Yuki Naoi, Kaori Sano, Yukie Katayama, Tsutomu Omatsu, Mami Oba, Shoichi Sakaguchi, Junsuke Shirai, Tetsuya Mizutani & Makoto Nagai

  6. Department of Microbiology and Infection Control, Osaka Medical College, Osaka, 569-8686, Japan

    Shoichi Sakaguchi

  7. Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan

    Tetsuya Furuya & Junsuke Shirai

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  1. Fujiko Sunaga
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Contributions

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.

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Correspondence to Makoto Nagai.

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Supplementary Fig. 1

. Sequence read depth of the contigs generated from the de novo sequence assembly. Mapping reads were conducted with regard to the contig using the CLC Genomics Workbench with the strictest parameter settings (mismatch cost, 2; insertion cost, 3; deletion cost, 3; length function, 0.9; and similarity function, 0.9) (XLSX 40 KB)

Supplementary Fig. 2

. Genome analysis of the 5′ UTR at the nucleotide positions 169–443 in PSV V13/1957/GBR (Accession No. NC_003987), corresponding to that of IRES stem-loop domains II and III of Japanese PSVs using PSVs from the DDBJ/EMBL/GenBank database. a Alignment of nt sequences of the 5′ UTR (nucleotide position 169–443 of PSV V13/1957/GBR) of PSVs. b Secondary structure prediction of the IRES within the 5′ UTR of PSVs. The core domains II and III are shown (XLSX 36 KB)

Supplementary Fig. 3. a

Genome structure of PSV. b–e Similarity plots of the entire genomes of Japanese PSVs, constructed using a sliding window of 200 nt and a moving step size of 20 nt (upper). Recombination breakpoint analysis of Japanese PSVs (lower). Recombination breakpoints are indicated using black arrows (PPTX 14711 KB)

Supplementary Fig. 4

. A phylogenetic tree constructed based on the nt sequences from the complete P1 region of 23 PSVs detected in this study, using 52 PSV sequences from the DDBJ/EMBL/GenBank database. The phylogenetic tree was constructed by the maximum likelihood method using MEGA7, and bootstrap values (1000 replicates) > 70 are shown. The bar represents a corrected genetic distance. ● Denotes PSVs detected in the present study. PSVs detected in Japan, China, South Korea, the USA, German, France, the UK, and India are shows in red, blue, yellow, green, black, light green, purple, and brown, respectively (PPTX 4548 KB)

Supplementary Table 1

Pairwise nucleotide sequence identities of the VP1 region (lower left) and 3CD region (upper right) between porcine sapeloviruses; the VP1 and 3CD regions, which showed sequence identities of ≥ 82.5% and ≥ 91.5%, are shown in yellow and red colors, respectively (PPTX 4089 KB)

Supplementary Table 2

Pairwise amino acid sequence identities of the VP1 region (lower left) and 3CD region (upper right) between porcine sapeloviruses. The VP1 and 3CD regions, which showed sequence identities of ≥ 89.0% and ≥ 98.8%, are presented in yellow and red, respectively (PPTX 54 KB)

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Sunaga, F., Masuda, T., Ito, M. et al. Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses. Virus Genes 55, 198–208 (2019). https://doi.org/10.1007/s11262-019-01640-8

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