Escape from recognition of SARS-CoV-2 variant spike epitopes but overall preservation of T cell immunity

  1. Catherine Riou
  2. Roanne Keeton
  3. Thandeka Moyo-Gwete
  4. Tandile Hermanus
  5. Prudence Kgagudi
  6. Richard Baguma
  7. Ziyaad Valley-Omar
  8. Mikhail Smith
  9. Houriiyah Tegally
  10. Deelan Doolabh
  11. Arash Iranzadeh
  12. Lynn Tyers
  13. Hygon Mutavhatsindi
  14. Marius B. Tincho
  15. Ntombi Benede
  16. Gert Marais
  17. Lionel R. Chinhoyi
  18. Mathilda Mennen
  19. Sango Skelem
  20. Elsa du Bruyn
  21. Cari Stek
  22. South African cellular immunity network
  23. Tulio de Oliveira
  24. Carolyn Williamson
  25. Penny L. Moore
  26. Robert J. Wilkinson
  27. Ntobeko A. B. Ntusi
  28. Wendy A. Burgers

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Abstract

SARS-CoV-2 variants that escape neutralization and potentially affect vaccine efficacy have emerged. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is incompletely understood. We assessed neutralizing antibody and T cell responses in 44 South African COVID-19 patients either infected with the Beta variant (dominant from November 2020 to May 2021) or infected before its emergence (first wave, Wuhan strain) to provide an overall measure of immune evasion. We show that robust spike-specific CD4 and CD8 T cell responses were detectable in Beta-infected patients, similar to first-wave patients. Using peptides spanning the Beta-mutated regions, we identified CD4 T cell responses targeting the wild-type peptides in 12 of 22 first-wave patients, all of whom failed to recognize corresponding Beta-mutated peptides. However, responses to mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3 of 44) mounted CD8 responses that targeted the mutated regions. Among the spike epitopes tested, we identified three epitopes containing the D215, L18, or D80 residues that were specifically recognized by CD4 T cells, and their mutated versions were associated with a loss of response. This study shows that despite loss of recognition of immunogenic CD4 epitopes, CD4 and CD8 T cell responses to Beta are preserved overall. These observations may explain why several vaccines have retained the ability to protect against severe COVID-19 even with substantial loss of neutralizing antibody activity against Beta.

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  1. Version published to 10.1126/scitranslmed.abj6824
  2. ScreenIT

    SciScore for 10.1101/2021.06.03.21258307: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study was approved by the University of Cape Town Human Research Ethics Committee (HREC: 207/2020 and R021/2020) and electronic or written informed consent was obtained from all participants.
    Consent: The study was approved by the University of Cape Town Human Research Ethics Committee (HREC: 207/2020 and R021/2020) and electronic or written informed consent was obtained from all participants.
    Field Sample Permit: Isolation of peripheral blood mononuclear cells (PBMC): Blood was collected in heparin tubes and processed within 3 hours of collection.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    All stimulations were performed in the presence of Brefeldin A (10 µg/mL, Sigma-Aldrich, St Louis, MO, USA) and co-stimulatory antibodies against CD28 (clone 28.2) and CD49d (clone L25) (1 µg/mL each; BD Biosciences, San Jose, CA, USA).
    CD28
    suggested: (BD Biosciences Cat# 347690, RRID:AB_647457)
    CD49d
    suggested: None
    After 16 hours of stimulation, cells were washed, stained with LIVE/DEAD™ Fixable Near-IR Stain (Invitrogen, Carlsbad, CA, USA) and subsequently surface stained with the following antibodies: CD4 BV785 (OKT4, Biolegend, San Diego, CA, USA), CD8 BV510 (RPA-8, Biolegend), PD-1 PE (J105, eBioscience, San Diego, CA, USA).
    CD4
    suggested: None
    OKT4
    suggested: (BD Biosciences Cat# 566804, RRID:AB_2869877)
    CD8
    suggested: (BioLegend Cat# 344731, RRID:AB_2564623)
    PD-1 PE
    suggested: (Thermo Fisher Scientific Cat# 12-2799-41, RRID:AB_10597751)
    CB6 and CA1monoclonal antibodies were used as controls.
    CB6
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Subsequently, 1×104 HEK293T cells engineered to over-express ACE-2, kindly provided by Dr Michael Farzan (Scripps Research Institute), were added and the incubated at 37°C, 5% CO2 for 72 hours, upon which the luminescence of the luciferase gene was measured.
    HEK293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Mutations were confirmed visually with bam files using Geneious software (Biomatters Ltd, New Zealand).
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    FlowJo LLC, Ashland, OR, USA)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    SARS-CoV-2 pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with the SARS-CoV-2 614G spike (D614G) or SARS-CoV-2 501Y.V2 spike (L18F, D80A, D215G, K417N, E484K, N501Y, A701V, 242-244 del
    SARS-CoV-2
    suggested: (BioLegend Cat# 944703, RRID:AB_2890874)
    Statistical analyses: 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: Thank you for sharing your data.

    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 10.1101/2021.06.03.21258307v1 on medRxiv