SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses

  1. Debashree Chatterjee
  2. Alexandra Tauzin
  3. Lorie Marchitto
  4. Shang Yu Gong
  5. Marianne Boutin
  6. Catherine Bourassa
  7. Guillaume Beaudoin-Bussières
  8. Yuxia Bo
  9. Shilei Ding
  10. Annemarie Laumaea
  11. Dani Vézina
  12. Josée Perreault
  13. Laurie Gokool
  14. Chantal Morrisseau
  15. Pascale Arlotto
  16. Éric Fournier
  17. Aurélie Guilbault
  18. Benjamin Delisle
  19. Inès Levade
  20. Guillaume Goyette
  21. Gabrielle Gendron-Lepage
  22. Halima Medjahed
  23. Gaston De Serres
  24. Cécile Tremblay
  25. Valérie Martel-Laferrière
  26. Daniel E. Kaufmann
  27. Renée Bazin
  28. Jérémie Prévost
  29. Sandrine Moreira
  30. Jonathan Richard
  31. Marceline Côté
  32. Andrés Finzi

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.celrep.2022.110429
  2. ScreenIT

    SciScore for 10.1101/2021.12.21.473679: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Data and code availability: EXPERIMENTAL MODEL AND SUBJECT DETAILS: 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 variableHuman subjects: The study was conducted in 10 SARS-CoV-2 naïve individuals (3 males and 7 females; age range : 40-59 years) vaccinated with a long interval, 12 SARS-CoV-2 naïve individuals (8 males and 4 females; age range : 24-60 years) vaccinated with a short interval and 10 SARS-CoV-2 previously-infected individuals (6 males and 4 females; age range : 39-65 years) vaccinated with a long interval.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Alexa Fluor-647-conjugated goat anti-human Abs (Invitrogen) were used as secondary antibodies to detect plasma binding in flow cytometry experiments.
    anti-human Abs ( Invitrogen )
    suggested: None
    The conformationally-independent anti-S2 antibody CV3-25 was used to normalize Spike expression, as reported (Gong et al., 2021; Li et al., 2021; Prevost et al., 2021; Ullah et al., 2021).
    anti-S2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: 293T human embryonic kidney cells (obtained from ATCC) were maintained at 37°C under 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Wisent) containing 5% fetal bovine serum (FBS) (VWR) and 100 μg/ml of penicillin-streptomycin (Wisent).
    293T
    suggested: None
    The 293T-ACE2 cell line was previously reported (Prévost et al., 2020).
    293T-ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    The plasmids encoding the B.1.1.529 Spike was 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_127347)
    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)
    Virus neutralization assay: To produce SARS-CoV-2 pseudoviruses, 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated S glycoprotein (D614G, Alpha, Beta, Gamma, Delta or Omicron) at a ratio of 10:1.
    pNL4.3
    suggested: None
    Software and Algorithms
    SentencesResources
    Samples were acquired on a LSR II cytometer (BD Biosciences), and data analysis was performed using FlowJo v10.7.1 (Tree Star).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistics were analyzed using GraphPad Prism version 8.0.1 (GraphPad, San Diego, CA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    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: 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 10.1101/2021.12.21.473679 on bioRxiv