Linear epitope landscape of the SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients

  1. Yang Li
  2. Ming-liang Ma
  3. Qing Lei
  4. Feng Wang
  5. Wei Hong
  6. Dan-yun Lai
  7. Hongyan Hou
  8. Zhao-wei Xu
  9. Bo Zhang
  10. Hong Chen
  11. Caizheng Yu
  12. Jun-biao Xue
  13. Yun-xiao Zheng
  14. Xue-ning Wang
  15. He-wei Jiang
  16. Hai-nan Zhang
  17. Huan Qi
  18. Shu-juan Guo
  19. Yandi Zhang
  20. Xiaosong Lin
  21. Zongjie Yao
  22. Jiaoxiang Wu
  23. Huiming Sheng
  24. Yanan Zhang
  25. Hongping Wei
  26. Ziyong Sun
  27. Xionglin Fan
  28. Sheng-ce Tao

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Abstract

No abstract available

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  1. Version published to 10.1016/j.celrep.2021.108915
  2. ScreenIT

    SciScore for 10.1101/2020.07.13.20152587: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Patients and samples: The study was approved by the Ethical Committee of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (IRB ID:TJ-C20200128) Written informed consent was obtained from all participants enrolled in this study.
    Consent: Patients and samples: The study was approved by the Ethical Committee of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (IRB ID:TJ-C20200128) Written informed consent was obtained from all participants enrolled in this study.
    RandomizationA few conjugates were randomly selected for examination by SDS-PAGE.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Peptide microarray fabrication: The peptide-BSA conjugates as well as S1 protein, RBD protein and N protein of SARS-CoV-2, along with the negative (BSA) and positive controls (anti-Human IgG and IgM antibody), were printed in triplicate on PATH substrate slide (Grace Bio-Labs, Oregon, USA) to generate identical arrays in a 1 x 7 subarray format using Super Marathon printer (Arrayjet, UK).
    IgM
    suggested: None
    The arrays were washed with 1×PBST and bound antibodies were detected by incubating with Cy3 - conjugated goat anti-human IgG and Alexa Fluor 647-conjugated donkey anti-human IgM (Jackson ImmunoResearch, PA, USA), which were diluted for 1: 1,000 in 1×PBST.
    anti-human IgG
    suggested: (Bio-Rad Cat# MCA647F, RRID:AB_808612)
    anti-human IgM
    suggested: None
    Structure analysis: The spike protein structures (PDB ID: 6×6P and 6VYB), RBD-ACE2 structure (PDB ID: 6M0J) and antibodies-RBD complex structure (PDB ID: 7C01, 7BWJ, 7BYR, 6W41 and 6WPT) were used to analyze the structural details of the epitopes identified from the peptide microarray.
    antibodies-RBD
    suggested: None
    Software and Algorithms
    SentencesResources
    Structural analysis was processed in Pymol.
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    The alignment and homology analysis of 7 human coronaviruses and one bat coronavirus was generated by ClustalW algorithm from EMBL-EBI (https://www.ebi.ac.uk/Tools/msa/clustalo/).
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    https://www.ebi.ac.uk/Tools/msa/clustalo/
    suggested: (Clustal Omega, RRID:SCR_001591)

    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: We detected the following sentences addressing limitations in the study:
    One limitation of this study is that only short peptides were involved. Though linear epitopes are nicely represented, conformational epitopes may not, for example, for RBD region, which is highly immunogenic, only 3 linear epitopes of moderate immunogenicity were identified. To overcome this limitation, one way is to synthesize longer peptides which may retain some conformational information (31). It is necessary to point out that for the linear epitopes that we identified, they are highly physiologically relevant, since all of them were revealed through the analysis of sera from COVID-19 patient. Our study presents the first IgG linear epitope landscape of Spike protein, which could only be enabled by analyzing a large cohort of samples using a systematic approach, such as the peptide microarray of full coverage of Spike protein. According to the landscape, it is obvious that Spike protein is highly immunogenic, there are many epitopes on the protein, and these epitopes are not evenly distributed across Spike protein. Among the 19 immunogenic peptides (Table S3), some may be good candidates for developing neutralization antibodies or vaccines, some may cause ADE, if any. The rest of the peptides may have no direct biological function, but serve only as neutral immunodominant epitopes that could not trigger neutralization activity and ADE. We believe that most of the 19 immunogenic peptides (Table S3) are worth further testing in animal model to identify which peptides can s...

    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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  3. Version published to 10.1101/2020.07.13.20152587v1 on medRxiv