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Ablation of CD8+ T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3

Author

Listed:
  • Srividhya Swaminathan

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

  • Katie E. Lineburg

    (QIMR Berghofer Medical Research Institute)

  • Archana Panikkar

    (QIMR Berghofer Medical Research Institute)

  • Jyothy Raju

    (QIMR Berghofer Medical Research Institute)

  • Lawton D. Murdolo

    (La Trobe University)

  • Christopher Szeto

    (La Trobe University
    Monash University)

  • Pauline Crooks

    (QIMR Berghofer Medical Research Institute)

  • Laetitia Texier

    (QIMR Berghofer Medical Research Institute)

  • Sweera Rehan

    (QIMR Berghofer Medical Research Institute)

  • Michael J. Dewar-Oldis

    (La Trobe University)

  • Peter J. Barnard

    (La Trobe University)

  • George R. Ambalathingal

    (QIMR Berghofer Medical Research Institute)

  • Michelle A. Neller

    (QIMR Berghofer Medical Research Institute)

  • Kirsty R. Short

    (The University of Queensland)

  • Stephanie Gras

    (La Trobe University
    Monash University)

  • Rajiv Khanna

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

  • Corey Smith

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

Abstract

The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells are less likely to be affected by changes in Omicron. However, the complexity of human leukocyte antigen genetics and its impact upon immunodominant T cell epitope selection suggests that the maintenance of T cell immunity may not be universal. In this study, we describe the impact that changes in Omicron BA.1, BA.2 and BA.3 have on recognition by spike-specific T cells. These T cells constitute the immunodominant CD8+ T cell response in HLA-A*29:02+ COVID-19 convalescent and vaccinated individuals; however, they fail to recognize the Omicron-encoded sequence. These observations demonstrate that in addition to evasion of antibody-mediated immunity, changes in Omicron variants can also lead to evasion of recognition by immunodominant T cell responses.

Suggested Citation

  • Srividhya Swaminathan & Katie E. Lineburg & Archana Panikkar & Jyothy Raju & Lawton D. Murdolo & Christopher Szeto & Pauline Crooks & Laetitia Texier & Sweera Rehan & Michael J. Dewar-Oldis & Peter J., 2022. "Ablation of CD8+ T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3," Nature Communications, Nature, vol. 13(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34180-1
    DOI: 10.1038/s41467-022-34180-1
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