Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2

  1. Zhe Liu
  2. Huanying Zheng
  3. Huifang Lin
  4. Mingyue Li
  5. Runyu Yuan
  6. Jinju Peng
  7. Qianling Xiong
  8. Jiufeng Sun
  9. Baisheng Li
  10. Jie Wu
  11. Lina Yi
  12. Xiaofang Peng
  13. Huan Zhang
  14. Wei Zhang
  15. Ruben J. G. Hulswit
  16. Nick Loman
  17. Andrew Rambaut
  18. Changwen Ke
  19. Thomas A. Bowden
  20. Oliver G. Pybus
  21. Jing Lu

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Abstract

The spike protein determines the infectivity and host range of coronaviruses. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has two unique features in its spike protein, the receptor binding domain and an insertion of 12 nucleotides at the S1/S2 boundary resulting in a furin-like cleavage site. Here, we identified two deletion variants of SARS-CoV-2 that either directly affect the furin-like cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN), and we investigated these deletions in cell isolates and clinical samples. The absence of the polybasic cleavage site in SARS-CoV-2 did not affect virus replication in Vero or Vero-E6 cells. Our data indicate the PRRAR sequence and the flanking QTQTN sequence are not fixed in vitro; thus, there appears to be distinct selection pressures on SARS-CoV-2 sequences in vitro and in vivo . Further investigation of the mechanism of generating these deletion variants and their infectivity in different animal models would improve our understanding of the origin and evolution of this virus.

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  1. Version published to 10.1128/jvi.00790-20
  2. ScreenIT

    SciScore for 10.1101/2020.03.31.015941: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your data.

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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.

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  3. Version published to 10.1101/2020.03.31.015941v1 on bioRxiv