SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

  1. Emanuele Andreano
  2. Giulia Piccini
  3. Danilo Licastro
  4. Lorenzo Casalino
  5. Nicole V. Johnson
  6. Ida Paciello
  7. Simeone Dal Monego
  8. Elisa Pantano
  9. Noemi Manganaro
  10. Alessandro Manenti
  11. Rachele Manna
  12. Elisa Casa
  13. Inesa Hyseni
  14. Linda Benincasa
  15. Emanuele Montomoli
  16. Rommie E. Amaro
  17. Jason S. McLellan
  18. Rino Rappuoli

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Abstract

This work shows that, under strong immune pressure, SARS-CoV-2 can use mutations in both the N-terminal domain and the receptor-binding domain to escape potent polyclonal neutralizing responses. Indeed, after a long period under immune selective pressure, SARS-CoV-2 evolved to evade the immunity of a potent polyclonal serum from a COVID-19 convalescent donor. Only three mutations were sufficient to generate this escape variant. The new virus was resistant to 70% of the neutralizing antibodies tested and had a decreased susceptibility to all convalescent sera. Our data predict that, as the immunity in the population increases, following infection and vaccination, new variants will emerge, and therefore vaccines and monoclonal antibodies need to be developed to address them.

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  1. Version published to 10.1073/pnas.2103154118
  2. ScreenIT

    SciScore for 10.1101/2020.12.28.424451: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Samples were collected from convalescent donors who gave their written consent.
    IRB: The study was approved by local ethics committees (Parere 18_2020 in Rome and Parere 17065 in Siena) and conducted according to good clinical practice in accordance with the declaration of Helsinki (European Council 2001, US Code of Federal Regulations, ICH 1997).
    RandomizationThis study was unblinded and not randomized.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Following, 25 μL/well of alkaline phosphatase-conjugated goat anti-human IgG (Sigma-Aldrich) was used as secondary antibodies.
    anti-human IgG
    suggested: None
    In detail, two models of the PT188-EM spike NTD (residues 13-308) were built starting from two different cryo-EM structures of the wild type S protein as templates: (i) one bearing a completely resolved NTD (PDB ID: 7JJI (7)), which includes all the loops from N1 to N5, and (ii) one bound to the antibody 4A8 (PDB ID: 7C2L (8)), which presents only one small gap within the N5 loop.
    N5
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    18-24 hours before execution of the viral escape assay, plates and propagation flasks containing a standard concentration of Vero E6 cells were prepared in complete DMEM medium supplemented with 2% FBS and incubated at 37°C, 5% CO2 until use.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    Sequenced reads were quality trimmed using Trimmomatic software during data analysis.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Only good quality reads were mapped against SARS-CoV-2_human_ITA_INMI1_2020 GenBank: MT066156.1 using BWA software with default parameters.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Data were collected by the LightCycler software during the annealing phase of each cycle of amplification.
    LightCycler
    suggested: (LightCycler Software, RRID:SCR_012155)
    CTF estimation and particle picking were performed using cisTEM (5), and particle stacks were exported to cryoSPARC v2 (6) for 2D classification, ab initio 3D reconstruction, and heterogeneous refinement.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    The final set up was done with PSFGEN and VMD (16), whereas MD simulations were run on TACC Frontera computer facility using NAMD 2.14 (18) and CHARMM36m force fields to refine the models (19–21).
    NAMD
    suggested: (NAMD, RRID:SCR_014894)

    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 17. 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. ScreenIT

    SciScore for 10.1101/2020.12.28.424451: (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.Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Every day, for four consecutive days, a titration plate was prepared and optically assessed after 72 hours of incubation to evaluate the CPE effect on Vero E6 cells and viral titer.
    Vero E6
    suggested: RRID:CVCL_XD71)

    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 used on page 17. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

  4. Version published to 10.1101/2020.12.28.424451 on bioRxiv