SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals

  1. Simone I. Richardson
  2. Vimbai Sharon Madzorera
  3. Holly Spencer
  4. Nelia P. Manamela
  5. Mieke A. van der Mescht
  6. Bronwen E. Lambson
  7. Brent Oosthuysen
  8. Frances Ayres
  9. Zanele Makhado
  10. Thandeka Moyo-Gwete
  11. Nonkululeko Mzindle
  12. Thopisang Motlou
  13. Amy Strydom
  14. Adriano Mendes
  15. Houriiyah Tegally
  16. Zelda de Beer
  17. Talita Roma de Villiers
  18. Annie Bodenstein
  19. Gretha van den Berg
  20. Marietjie Venter
  21. Tulio de Oliviera
  22. Veronica Ueckermann
  23. Theresa M. Rossouw
  24. Michael T. Boswell
  25. Penny L. Moore

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Abstract

No abstract available

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  1. Version published to 10.1016/j.chom.2022.03.029
  2. Version published to 10.1101/2022.02.10.22270789v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2022.02.10.22270789: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics approval was received from the University of Pretoria, Human Research Ethics Committee (Medical) (247/2020).
    Consent: Written informed consent was obtained from all participants.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Antibody-dependent cellular phagocytosis (ADCP) assay: Avitagged SARS-CoV-2 spikes were biotinylated using the BirA biotin-protein ligase standard reaction kit (Avidity, LLC) and coated onto fluorescent neutravidin beads as previously described32.
    Antibody-dependent cellular phagocytosis (ADCP
    suggested: None
    Antibody-dependent cellular cytotoxicity (ADCC) assay: The ability of plasma antibodies to cross-link and signal through FcγRIIIa (CD16) and spike expressing cells or SARS-CoV-2 protein was measured as a proxy for ADCC.
    CD16
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 antigens: For ELISA and ADCP assays, SARS-CoV-2 original and Beta variant full spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del), Delta (T19R, 156-157del, R158G, L452R, T478K, D614G, P681R and D950N) and Omicron (A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, 214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) proteins were expressed in Human Embryonic Kidney (HEK) 293F suspension cells by transfecting the cells with the respective expression plasmid.
    HEK
    suggested: RRID:CVCL_6642)
    Phagocytosis score was calculated as the percentage of THP-1 cells that engulfed fluorescent beads multiplied by the geometric mean fluorescence intensity of the population less the no antibody control.
    THP-1
    suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
    For spike assays, HEK293T cells were transfected with 5μg of SARS-CoV-2 spike plasmids using PEI-MAX 40,000 (Polysciences) and incubated for 2 days at 37°C.
    HEK293T
    suggested: None
    Jurkat-Lucia™ NFAT-CD16 cells (Invivogen) (2×105 cells/well and 1×105 cells/well for spike and other protein respectively) were added and incubated for 24 hours at 37°C, 5% CO2.
    NFAT-CD16
    suggested: RRID:CVCL_A7ZT)
    Recombinant DNA
    SentencesResources
    Spike plasmid and Lentiviral Pseudovirus Production: The SARS-CoV-2 Wuhan-1 spike, cloned into pCDNA3.1 was mutated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and NEBuilder HiFi DNA Assembly Master Mix (NEB) to include D614G (original) or lineage defining mutations for Beta (L18F, D80A, D215G, 242-244del, K417N, E484K, N501Y, D614G and A701V), Delta (T19R, 156-157del, R158G, L452R, T478K, D614G, P681R and D950N), C.1.2. (P9L, P25L, C136F, Δ144, R190S, D215G, Δ242-243, Y449H, E484K, N501Y, L585F, D614G, H655Y, N679K, T716I, T859N) or Omicron (A67V, Δ69-70, T95I, G142D, Δ143-145, Δ211, L212I, 214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F)
    pCDNA3.1
    suggested: RRID:Addgene_79663)
    Other pcDNA plasmids were used for the ADCC assay.
    pcDNA
    suggested: RRID:Addgene_66792)
    Software and Algorithms
    SentencesResources
    THP-1 cells were used for both the ADCP and ADCT assays and obtained from the AIDS Reagent Program, Division of AIDS, NIAID, NIH contributed by Dr. Li Wu and Vineet N. KewalRamani.
    AIDS Reagent Program
    suggested: None
    QUANTIFICATION AND STATISTICAL ANALYSIS: Analyses were performed in Prism (v9; GraphPad Software Inc, San Diego, CA, USA).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    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.
    • Thank you for including a protocol registration statement.

    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.

  4. Version published to 10.1101/2022.02.10.22270789v1 on medRxiv