Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes

  1. William N. Voss
  2. Yixuan J. Hou
  3. Nicole V. Johnson
  4. George Delidakis
  5. Jin Eyun Kim
  6. Kamyab Javanmardi
  7. Andrew P. Horton
  8. Foteini Bartzoka
  9. Chelsea J. Paresi
  10. Yuri Tanno
  11. Chia-Wei Chou
  12. Shawn A. Abbasi
  13. Whitney Pickens
  14. Katia George
  15. Daniel R. Boutz
  16. Dalton M. Towers
  17. Jonathan R. McDaniel
  18. Daniel Billick
  19. Jule Goike
  20. Lori Rowe
  21. Dhwani Batra
  22. Jan Pohl
  23. Justin Lee
  24. Shivaprakash Gangappa
  25. Suryaprakash Sambhara
  26. Michelle Gadush
  27. Nianshuang Wang
  28. Maria D. Person
  29. Brent L. Iverson
  30. Jimmy D. Gollihar
  31. John M. Dye
  32. Andrew S. Herbert
  33. Ilya J. Finkelstein
  34. Ralph S. Baric
  35. Jason S. McLellan
  36. George Georgiou
  37. Jason J. Lavinder
  38. Gregory C. Ippolito

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Abstract

Most analyses of the antibody responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have focused on antibodies cloned from memory B cells. This approach has led researchers to conclude that neutralizing antibodies (nAbs) primarily target the receptor-binding domain (RBD) of the virus's spike protein. Voss et al. took a different approach, using proteomic deconvolution of the serum immunoglobulin G antibody repertoire from four COVID-19 convalescent patients. They found that the nAb response was largely directed against epitopes such as the N-terminal domain (NTD), which lie outside the RBD. Several of these nAbs were shared among donors and targeted an NTD epitope that is frequently mutated by variants of concern.

Science , abg5268, this issue p. 1108

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  1. Version published to 10.1126/science.abg5268
  2. ScreenIT

    SciScore for 10.1101/2020.12.20.423708: (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 variableAt 12h before infection, twelve-month-old female BALB/c mice (n=5/group) were injected intraperitoneally with 200μg/mouse of mAb or PBS.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    ELISA: The methods for enzyme-linked immunosorbent assay to measure titers of anti-SARS-CoV-2 IgG plasma antibodies have been previously described4.
    anti-SARS-CoV-2 IgG
    suggested: None
    Antibody expression and purification: Cognate VH and VL antibody sequences of interest were ordered as gBlocks (Integrated DNA Technologies) and cloned into a customized pcDNA 3.4 vector containing a human IgG1 Fc region.
    VL
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Viral titers in the lung tissue were measured by plaque assay on Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Experimental Models: Organisms/Strains
    SentencesResources
    At 12h before infection, twelve-month-old female BALB/c mice (n=5/group) were injected intraperitoneally with 200μg/mouse of mAb or PBS.
    BALB/c
    suggested: None
    Software and Algorithms
    SentencesResources
    Sequences with ≥ 2 reads were clustered into clonal lineages defined by 90% CDRH3 amino acid identity using USEARCH10. LC-MS/MS search databases were prepared as previously described7, using custom Python scripts (available upon request).
    Python
    suggested: (IPython, RRID:SCR_001658)
    Movies were collected using SerialEM at 22,500X magnification with a corresponding calibrated pixel size of 1.1 Å2/ pixel.
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    Micrographs were then imported into cryoSPARC v2.15.0 for CTF-estimation, particle picking, 2D classification, ab initio reconstruction, heterogenous 3D refinement and homogenous refinement14.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    The model was built further and iteratively refined using a combination of Coot, Phenix, and ISOLDE18-20.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    Statistics: GraphPad Prism version 9.0.0 (GraphPad Software Inc., La Jolla, CA, USA) was used to conduct statistical analyses.
    Statistics: GraphPad Prism
    suggested: None
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 38. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

  3. Version published to 10.1101/2020.12.20.423708 on bioRxiv