Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes

  1. Winston A. Haynes
  2. Kathy Kamath
  3. Carolina Lucas
  4. John Shon
  5. Akiko Iwasaki

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Abstract

In 579 COVID patients’ samples collected between March and July of 2020, we examined the effects of non-synonymous mutations harbored by the circulating B.1.1.7 strain on linear antibody epitope signal for spike glycoprotein and nucleoprotein. At the antigen level, the mutations only substantially reduced signal in 0.5% of the population. Although some epitope mutations reduce measured signal in up to 6% of the population, these are not the dominant epitopes for their antigens. Given dominant epitope patterns observed, our data suggest that the mutations would not result in immune evasion of linear epitopes for a large majority of these COVID patients.

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  1. Rapid Reviews Infectious Diseases

    Gregory Towers

    Review 2: "Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes"

    This preprint reports that antibodies generated from infection with the Wuhan SARS-CoV-2 virus retain binding to linear epitopes of S and N protein from the B.1.1.7 variant. Reviewers deem these findings reliable and recommended validating these results with vaccinated samples.

  2. Rapid Reviews Infectious Diseases

    Debmalya Barh

    Review 1: "Impact of B.1.1.7 variant mutations on antibody recognition of linear SARS-CoV-2 epitopes"

    This preprint reports that antibodies generated from infection with the Wuhan SARS-CoV-2 virus retain binding to linear epitopes of S and N protein from the B.1.1.7 variant. Reviewers deem these findings reliable and recommended validating these results with vaccinated samples.

  4. ScreenIT

    SciScore for 10.1101/2021.01.06.20248960: (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

    Antibodies
    SentencesResources
    Antibody-bound bacterial clones were selected with 50 µL Protein A/G Sera-Mag SpeedBeads (GE Life Sciences, cat#17152104010350) (IgG) or by incubation with a biotinylated anti-human IgM antibody (Jackson ImmunoResearch, cat# 709-066-073) final assay dilution 1:100, followed by a second incubation with 50 ul Dynabead MyOne Streptavidin T1 conjugated magnetic beads (IgM) (Thermo-Fisher 65602).
    anti-human IgM
    suggested: (Jackson ImmunoResearch Labs Cat# 709-066-073, RRID:AB_2340508)

    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

    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.

  5. ScreenIT

    SciScore for 10.1101/2021.01.06.20248960: (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

    Antibodies
    SentencesResources
    Antibody-bound bacterial clones were selected with 50 µL Protein A/G Sera-Mag SpeedBeads (GE Life Sciences, cat#17152104010350) (IgG) or by incubation with a biotinylated anti-human IgM antibody (Jackson ImmunoResearch, cat# 709-066-073) final assay dilution 1:100, followed by a second incubation with 50 ul Dynabead MyOne
    anti-human IgM
    suggested: (Jackson ImmunoResearch Labs Cat# 709-066-073, RRID:AB_2340508)
    Experimental Models: Organisms/Strains
    SentencesResources
    PIWAS Epitope Score PIWAS Antigen Score PIWAS Epitope Score PIWAS Epitope Score Amino Acid Position N ●● ●● ● ●● ●●● ●● ●● ● ●● ●●● ● ● ●● ●●● ●● ●● ● ● ● ● ● ●●●● ●●●●● ● ● ● ● ● ●● ●●●● ● ●● ● ● ● ● ● ●●● ●● ●● ●● ●● ●●● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●●● ●● ● ● ●● ●●●● ● ● ●● ●● ● ● ● ●●● ●● ● ●●●● ● ● ●● ●● ●● ● ●● ●●● ● ●●● ● ● ● ● ●● ●● ●● ●● ●● ● ●● ● ●●● ● ●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●●● ●●●●● ●● ●●●●●● ●● ● ●●● ● ● ●● ●● ●●●● ● ● ● ● ●●● ●● ● ●●● ●● ● ● ● ● ● ●● ●●● ● ●● ●● ● ●●● ●● ● ●
    N ●● ●● ● ●● ●●● ●● ●● ● ●● ●●● ● ● ●● ●●● ●● ●● ● ● ● ● ● ●●●● ●●●●● ● ● ● ● ● ●● ●●●● ● ●● ● ● ● ● ● ●●● ●● ●● ●● ●● ●●● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●●● ●● ● ● ●● ●●●● ● ● ●● ●● ● ● ● ●●● ●● ● ●●●● ● ● ●● ●● ●● ● ●● ●●● ● ●●● ● ● ● ● ●● ●● ●● ●● ●● ● ●● ● ●●● ● ●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●●●●●●● ●●●●● ●● ●●●●●● ●● ● ●●● ● ● ●● ●● ●●●● ● ● ● ● ●●● ●● ● ●●● ●● ● ● ● ● ● ●● ●●● ● ●● ●● ● ●●● ●● ●
    suggested: None

    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.

    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.

  6. Version published to 10.1101/2021.01.06.20248960v1 on medRxiv