Virus Genes

, Volume 55, Issue 2, pp 198–208 | Cite as

Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses

  • Fujiko Sunaga
  • Tsuneyuki Masuda
  • Mika Ito
  • Masataka Akagami
  • Yuki Naoi
  • Kaori Sano
  • Yukie Katayama
  • Tsutomu Omatsu
  • Mami Oba
  • Shoichi Sakaguchi
  • Tetsuya Furuya
  • Hiroshi Yamasato
  • Yoshinao Ouchi
  • Junsuke Shirai
  • Tetsuya Mizutani
  • Makoto NagaiEmail author


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.


Complete genome analysis Japan Molecularly characterization Porcine feces Sapelovirus A 



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

Author 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.

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.

Informed consent

Not applicable.

Supplementary material

11262_2019_1640_MOESM1_ESM.xlsx (40 kb)
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)
11262_2019_1640_MOESM2_ESM.xlsx (37 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)
11262_2019_1640_MOESM3_ESM.pptx (14.4 mb)
Supplementary Fig. 3. a Genome structure of PSV. be 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)
11262_2019_1640_MOESM4_ESM.pptx (4.4 mb)
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)
11262_2019_1640_MOESM5_ESM.pptx (4 mb)
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)
11262_2019_1640_MOESM6_ESM.pptx (54 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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Fujiko Sunaga
    • 1
  • Tsuneyuki Masuda
    • 2
  • Mika Ito
    • 3
  • Masataka Akagami
    • 4
  • Yuki Naoi
    • 5
  • Kaori Sano
    • 5
  • Yukie Katayama
    • 5
  • Tsutomu Omatsu
    • 5
  • Mami Oba
    • 5
  • Shoichi Sakaguchi
    • 5
    • 6
  • Tetsuya Furuya
    • 7
  • Hiroshi Yamasato
    • 2
  • Yoshinao Ouchi
    • 4
  • Junsuke Shirai
    • 5
    • 7
  • Tetsuya Mizutani
    • 5
  • Makoto Nagai
    • 1
    • 5
    Email author
  1. 1.School of Veterinary MedicineAzabu UniversitySagamiharaJapan
  2. 2.Kurayoshi Livestock Hygiene Service CenterKurayoshiJapan
  3. 3.Ishikawa Nanbu Livestock Hygiene Service CenterKanazawaJapan
  4. 4.Kenpoku Livestock Hygiene Service CenterMitoJapan
  5. 5.Research and Education Center for Prevention of Global Infectious Disease of AnimalsTokyo University of Agriculture and TechnologyFuchuJapan
  6. 6.Department of Microbiology and Infection ControlOsaka Medical CollegeOsakaJapan
  7. 7.Cooperative Department of Veterinary Medicine, Faculty of AgricultureTokyo University of Agriculture and TechnologyFuchuJapan

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