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Complete genome sequencing and genetic analysis of a Japanese porcine torovirus strain detected in swine feces

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Abstract

We sequenced the complete genome of a porcine torovirus (PToV) strain from Japan for the first time. Whole-genome analysis revealed that this strain (Iba/2018) has a mosaic sequence composed of at least three genome backgrounds, related to US, Chinese and German PToV strains. Clear recombination breakpoints were detected in the M and HE coding regions. A similarity plot and structural analysis demonstrated that the HE coding region exhibits the highest diversity, and the most sequence variation was found in the lectin domain. PToVs were divided into two lineages in the HE region, whereas clear lineages were not found in other regions.

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Acknowledgements

This work was supported by JSPS KAKENHI (grant numbers 15K07718 and 18K05977).

Author information

Author notes

  1. Y. Fujii and Y. Kashima contributed equally to this work.

Authors and Affiliations

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

    Yuki Fujii, Yuki Kashima, Satoko Tsuzuku & Yoshinao Ouchi

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

    Fujiko Sunaga & Makoto Nagai

  3. Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan

    Hiroshi Aoki

  4. Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, 162-0052, Japan

    Kaori Sano

  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

    Ryo Imai, Yukie Katayama, Tsutomu Omatsu, Mami Oba, Tetsuya Mizutani & Makoto Nagai

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

    Tetsuya Furuya & Junsuke Shirai

  7. Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan

    Tomoichiro Oka

Authors
  1. Yuki Fujii
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Corresponding author

Correspondence to Makoto Nagai.

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Research involving human participants and/or animals

This study did not involve any human participants or animals.

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Supplementary material 1 (TXT 27 kb)

Supplementary Fig. 1

(A) Nucleotide sequence alignment of the M and HE coding regions of PToV/NPL/USA/2014, PToV/Iba/JPN/2018, and PToV/L00926/DEU/2014. (B) Recombination breakpoint analysis of PToV/NPL/USA/2014 vs. PToV/L00926/DEU/2014 (yellow curve), PToV/NPL/USA/2014 vs. PToV/Iba/JPN/2018 (blue curve), and PToV/L00926/DEU/2014 vs. PToV/Iba/JPN/2018 (purple curve) (C) Partial genome structure of torovirus. (PPTX 1174 kb)

Supplementary Fig. 2

Phylogenetic analysis based on the amino acid sequences of papain-like cysteine protease of Iba/2018 (denoted by ● and boldface) and those of previously reported toroviruses and enterovirus G strains obtained from the DDBJ/EMBL/GenBank databases. The phylogenetic tree was constructed by the maximum-likelihood method in MEGA7.0 with the best-fit model (JJT+I), and bootstrap values above 70 (1000 replicates) are shown. The bar represents amino acid substitutions per site (PPTX 45 kb)

Supplementary Fig. 3

RT-PCR analysis of Iba/2018. Specific primers were designed from the sequence obtained by the de novo assembly algorithm in CLC Genomics Workbench (PPTX 10395 kb)

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Fujii, Y., Kashima, Y., Sunaga, F. et al. Complete genome sequencing and genetic analysis of a Japanese porcine torovirus strain detected in swine feces. Arch Virol 165, 471–477 (2020). https://doi.org/10.1007/s00705-019-04514-4

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