SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity

  1. Simone I. Richardson
  2. Nelia P. Manamela
  3. Boitumelo M. Motsoeneng
  4. Haajira Kaldine
  5. Frances Ayres
  6. Zanele Makhado
  7. Mathilda Mennen
  8. Sango Skelem
  9. Noleen Williams
  10. Nancy J. Sullivan
  11. John Misasi
  12. Glenda G. Gray
  13. Linda-Gail Bekker
  14. Veronica Ueckermann
  15. Theresa M. Rossouw
  16. Michael T. Boswell
  17. Ntobeko A.B. Ntusi
  18. Wendy A. Burgers
  19. Penny L. Moore

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Abstract

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  3. Version published to 10.1016/j.xcrm.2022.100510
  4. ScreenIT

    SciScore for 10.1101/2021.11.05.21265853: (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.
    RandomizationSARS-CoV-2 spike genome sequencing: For wave 2 samples, sequencing of the spike was performed as previously described 24 using swabs obtained from 28 randomly collected Groote Schuur Hospital patients of which eight were included in this study.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    IgG or IgA secondary antibody was diluted to 1:3000 or 1:1000 respectively in blocking buffer and added to the plates followed by TMB substrate (Thermofisher Scientific).
    IgA
    suggested: None
    Antibody-dependent cellular phagocytosis (ADCP) assay: SARS-CoV-2 original or Beta spike was biotinylated using EZ link Sulfo-NHS-LC-Biotin kit (ThermoFisher) and coated on to fluorescent neutravidin beads as previously described 32.
    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
    Antibody-dependent cellular trogocytosis (ADCT) assay: ADCT was performed as described in and modified from a previously described study34.
    Antibody-dependent cellular trogocytosis (ADCT
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    , RBD original and Beta (K417N, E484K and N501Y, D614G) and NTD original and Beta (L18F, D80A, D215G and 242-244 del) 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)
    Pseudotyped lentiviruses were prepared by co-transfecting HEK293T cell line with either the SARS-CoV-2 ancestral variant spike (D614G) or the Beta spike plasmids in conjunction with a firefly luciferase encoding lentivirus backbone plasmid as previously described 24.
    HEK293T
    suggested: None
    Opsonized beads were incubated with the monocytic THP-1 cell line overnight, fixed and interrogated on the FACSAria II.
    THP-1
    suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
    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), Gamma (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F) or Delta (T19R, 156-157del, R158G, L452R, T478K, D614G, P681R and D950N).
    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
    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.
    • 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.

  5. Version published to 10.1101/2021.11.05.21265853v1 on medRxiv