Characterization of the SARS-CoV-2 Spike in an Early Prefusion Conformation

  1. Tingting Li
  2. Qingbing Zheng
  3. Hai Yu
  4. Dinghui Wu
  5. Wenhui Xue
  6. Yuyun Zhang
  7. Xiaofen Huang
  8. Lizhi Zhou
  9. Zhigang Zhang
  10. Zhenghui Zha
  11. Tingting Chen
  12. Zhiping Wang
  13. Jie Chen
  14. Hui Sun
  15. Tingting Deng
  16. Yingbin Wang
  17. Yixin Chen
  18. Qinjian Zhao
  19. Jun Zhang
  20. Ying Gu
  21. Shaowei Li
  22. Ningshao Xia

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Abstract

Pandemic coronavirus disease 2019 (COVID-19) is caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there are no efficacious vaccines or therapeutics that are urgently needed. We expressed three versions of spike (S) proteins—receptor binding domain (RBD), S1 subunit and S ectodomain—in insect cells. RBD appears monomer in solutions, whereas S1 and S associate into homotrimer with substantial glycosylation. The three proteins confer excellent antigenicity with six convalescent COVID-19 patient sera. Cryo-electron microscopy (cryo-EM) analyses indicate that the SARS-CoV-2 S trimer dominate in a unique conformation distinguished from the classic prefusion conformation of coronaviruses by the upper S1 region at lower position ~15 Å proximal to viral membrane. Such conformation is proposed as an early prefusion state for the SARS-CoV-2 spike that may broaden the knowledge of coronavirus and facilitate vaccine development.

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    SciScore for 10.1101/2020.03.16.994152: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    Unbound antibody was removed by five 5-min washes and the membrane was incubated with alkaline phosphatase-conjugated goat anti-mouse secondary antibody or goat anti-human IgG secondary antibody (Abcam, Cambridge, UK).
    anti-mouse
    suggested: None
    anti-human IgG
    suggested: None
    Horseradish peroxidase (HRP)-labeled mouse anti-human antibody (Abcam) was used as secondary antibody at 1:5,000 for 30 min.
    mouse anti-human antibody ( Abcam )
    suggested: None
    anti-human antibody
    suggested: None
    Software and Algorithms
    SentencesResources
    In all three constructs, the natural signal peptide (aa 1-14 analyzed by SignalP tool) was replaced with a gp67 secretion signal peptide at N-terminus.
    SignalP
    suggested: (SignalP, RRID:SCR_015644)
    The Half effective titers (ET50) was calculated by sigmoid trend fitting using GraphPad Prism software.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Particles were picked by the ‘Templete picker’ session of cryoSPARC v237.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)

    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

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  2. Version published to 10.1101/2020.03.16.994152v2 on bioRxiv
  3. Version published to 10.1101/2020.03.16.994152v1 on bioRxiv