Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C

  1. Kodai Abe
  2. Takako Shimura
  3. Toshiki Takenouchi
  4. Yuka W. Iwasaki
  5. Hirotsugu Ishizu
  6. Yoshifumi Uwamino
  7. Shunsuke Uno
  8. Jun Gotoh
  9. Natsuo Tachikawa
  10. Yuriko Takeuchi
  11. Junpei Katayama
  12. Hiroyuki Nozaki
  13. Susumu Fujii
  14. Shikou Seki
  15. Morio Nakamura
  16. Kazuhiro Uda
  17. Takahiko Misumi
  18. Jun Ishihara
  19. Kenichiro Yamada
  20. Toshio Kanai
  21. Shinji Murai
  22. Kazuhiro Araki
  23. Tamotsu Ebihara
  24. Haruhiko Shiomi
  25. Naoki Hasegawa
  26. Yuko Kitagawa
  27. Masayuki Amagai
  28. Makoto Suematsu
  29. Kenjiro Kosaki

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Objectives

Whole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan.

Methods

We performed whole genome sequencing in specimens of 198 COVID-19 patients at 13 collaborating hospitals in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions underwent to differentiate and classify the viral lineages.

Results

More than 90% of the strains belonged to Clade 20B and two lineages (B.1.1.284 and B.1.1.214) have been detected predominantly in the Kanto region. However, one sample from a COVID-19 patient in November 2020, belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in western United States. The patient had no history of overseas travel and no contact with anyone who had travelled abroad, suggesting that this strain appeared likely to have been imported from western United States, across the strict quarantine barrier.

Conclusion

B.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region and B.1.346 of clade 20C in one patient was probably imported from western United States. These results illustrate that a decentralized network of hospitals can be significantly advantageous for monitoring regional molecular epidemiologic trends.

Highlights

  • · Whole SARS-CoV-2 genome sequencing is useful for infection control

  • · B.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region

  • · B.1.346 of Clade 20C was detected in one COVID-19 patient in November

  • · Molecular genomic data sharing provides benefits to public health against COVID-19

    • Article activity feed

    1. ScreenIT

      SciScore for 10.1101/2021.01.29.21250798: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      Institutional Review Board StatementIRB: Study design and patients: The study protocol was approved by the Institutional Review Board of Keio University School of Medicine (approval number: 20200062) with each collaborating hospitals’ review board and was conducted according to the principles of the Declaration of Helsinki.
      Randomizationnot detected.
      Blindingnot detected.
      Power Analysisnot detected.
      Sex as a biological variablenot detected.

      Table 2: Resources

      Software and Algorithms
      SentencesResources
      Paired end sequencing was performed on the MiSeq platform (Illumina, CA).
      MiSeq
      suggested: (A5-miseq, RRID:SCR_012148)
      The bioinformatic pipeline used in this study, “Mutation calling pipeline for amplicon-based sequencing of the SARS-CoV-2 viral genome,” is available at https://cmg.med.keio.ac.jp/sars-cov-2/.
      bioinformatic
      suggested: (QFAB Bioinformatics, RRID:SCR_012513)
      All single nucleotide substitutions including non-synonymous and synonymous mutations were annotated by the ANNOVAR software and were assessed using VarSifter (https://research.nhgri.nih.gov/software/VarSifter/).
      ANNOVAR
      suggested: (ANNOVAR, RRID:SCR_012821)
      Genetic clade or lineage naming in phylogenic tree analyses: A phylogenetic tree analysis was performed locally using the Augur program available from Nextstrain (https://nextstrain.org/) and genome sequence data obtained in the currently reported study as well as data available from the global database EpiCov hosted at GISAID (Hadfield, et al., 2020).
      Augur
      suggested: None

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

      Results from JetFighter: We did not find any issues relating to colormaps.

      Results from rtransparent:
      • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
      • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
      • No protocol registration statement was detected.

      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    2. Version published to 10.1101/2021.01.29.21250798v1 on medRxiv
    3. Version published to 10.2302/kjm.2021-0005-oa