Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity

  1. Shang Yu Gong
  2. Debashree Chatterjee
  3. Jonathan Richard
  4. Jérémie Prévost
  5. Alexandra Tauzin
  6. Romain Gasser
  7. Yuxia Bo
  8. Dani Vézina
  9. Guillaume Goyette
  10. Gabrielle Gendron-Lepage
  11. Halima Medjahed
  12. Michel Roger
  13. Marceline Côté
  14. Andrés Finzi

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Abstract

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  1. Version published to 10.1016/j.virol.2021.09.001
  2. ScreenIT

    SciScore for 10.1101/2021.08.04.455140: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: The presence of the desired mutations was determined by automated DNA sequencing.

    Table 2: Resources

    Antibodies
    SentencesResources
    Alexa Fluor-647-conjugated goat anti-human Abs (Invitrogen) were used as secondary antibodies to detect ACE2-Fc and plasma binding in flow cytometry experiments.
    anti-human Abs ( Invitrogen )
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    The 293T-ACE2 cell line was previously described (Prévost et al., 2020) and was maintained in medium supplemented with 2 µg/mL of puromycin (Millipore Sigma).
    293T-ACE2
    suggested: None
    Virus neutralization assay: 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated Spike glycoprotein (D614G, B.1.1.7, P.1, B.1.351, B.1.429, B.1.526, B.1.617, B.1.617.1, B.1.617.2) at a ratio of 10:1.
    293T
    suggested: None
    Two days post-transfection, 293T-Spike cells were stained with the CV3-25 Ab, ACE2-Fc or plasma from SARS-CoV-2-naïve or recovered donors.
    293T-Spike
    suggested: None
    Recombinant DNA
    SentencesResources
    Plasmids encoding B.1.617, B.1.617.1, B.1.617.2 Spikes were generated by overlapping PCR using a codon-optimized wild-type SARS-CoV-2 Spike gene (GeneArt, ThermoFisher) that was synthesized (Biobasic) and cloned in pCAGGS as a template.
    pCAGGS
    suggested: RRID:Addgene_18926)
    Plasmids encoding B.1.429, D614G and other SARS-CoV-2 Spike single mutations were generated using the QuickChange II XL site-directed mutagenesis protocol (Stratagene) and the pCG1-SARS-CoV-2-S plasmid kindly provided by Stefan Pöhlmann.
    pCG1-SARS-CoV-2-S
    suggested: None
    Virus neutralization assay: 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated Spike glycoprotein (D614G, B.1.1.7, P.1, B.1.351, B.1.429, B.1.526, B.1.617, B.1.617.1, B.1.617.2) at a ratio of 10:1.
    pNL4.3
    suggested: None
    Cell surface staining and flow cytometry analysis: 293T were transfected with full length SARS-CoV-2 Spikes and a green fluorescent protein (GFP) expressor (pIRES2-eGFP; Clontech) using the calcium-phosphate method.
    pIRES2-eGFP
    suggested: RRID:Addgene_14998)
    Software and Algorithms
    SentencesResources
    Samples were acquired on a LSRII cytometer (BD Biosciences), and data analysis was performed using FlowJo v10.7.1 (Tree Star).
    BD Biosciences
    suggested: (BD Biosciences, RRID:SCR_013311)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.08.04.455140v1 on bioRxiv