Goldberg, Y. et al. Protection and waning of natural and hybrid immunity to SARS-CoV-2. N. Engl. J. Med. 386, 2201–2212 (2022).

Article  CAS  PubMed  Google Scholar 

Suarez Castillo, M., Khaoua, H. & Courtejoie, N. Vaccine-induced and naturally-acquired protection against Omicron and Delta symptomatic infection and severe COVID-19 outcomes, France, December 2021 to January 2022. Euro Surveill. 27, 2200250 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Qu, P. et al. Durability of booster mRNA vaccine against SARS-CoV-2 BA.2.12.1, BA.4, and BA.5 subvariants. N. Engl. J. Med. 387, 1329–1331 (2022).

Article  Google Scholar 

Lim, J. M. E. et al. SARS-CoV-2 breakthrough infection in vaccinees induces virus-specific nasal-resident CD8+ and CD4+ T cells of broad specificity. J. Exp. Med. 219, e2020780 (2022).

Article  Google Scholar 

Peng, Y. et al. Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat. Immunol. 21, 1336–1345 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tavukcuoglu, E., Horzum, U., Cagkan Inkaya, A., Unal, S. & Esendagli, G. Functional responsiveness of memory T cells from COVID-19 patients. Cell. Immunol. 365, 104363 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rodda, L. B. et al. Functional SARS-CoV-2-specific immune memory persists after mild COVID-19. Cell 184, 169–183 (2021).

Article  CAS  PubMed  Google Scholar 

Dykema, A. G. et al. SARS-CoV-2 vaccination diversifies the CD4+ spike-reactive T cell repertoire in patients with prior SARS-CoV-2 infection. eBioMedicine 80, 104048 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Minervina, A. A. et al. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells. Nat. Immunol. 23, 781–790 (2022).

Article  CAS  PubMed  Google Scholar 

Kared, H. et al. Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults. Nat. Commun. 13, 4165 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Altarawneh, H. N. et al. Effects of previous infection and vaccination on symptomatic Omicron infections. N. Engl. J. Med. 387, 21–34 (2022).

Article  CAS  PubMed  Google Scholar 

Keeton, R. et al. T cell responses to SARS-CoV-2 spike cross-recognize Omicron. Nature 603, 488–492 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao, Y. et al. Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant. Nat. Med. 28, 472–476 (2022).

Article  CAS  PubMed  Google Scholar 

Dolton, G. et al. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 185, 2936–2951 (2022).

Article  CAS  PubMed Central  Google Scholar 

Naranbhai, V. et al. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 185, 1041–1051 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Müller, N. F. et al. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci. Transl. Med. 13, eabf0202 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Mueller, Y. M. et al. Stratification of hospitalized COVID-19 patients into clinical severity progression groups by immuno-phenotyping and machine learning. Nat. Commun. 13, 915 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Elyanow, R. et al. T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity. JCI Insight 7, e150070 (2022).

Article  PubMed  Google Scholar 

Zhang, J. Z. et al. Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nat. Biotechnol. 40, 1336–1340 (2022).

Article  CAS  PubMed Central  Google Scholar 

Johansson, A. M. et al. Cross-reactive and mono-reactive SARS-CoV-2 CD4+ T cells in prepandemic and COVID-19 convalescent individuals. PLoS Pathog. 17, e1010203 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boonyaratanakornkit, J. et al. Clinical, laboratory, and temporal predictors of neutralizing antibodies against SARS-CoV-2 among COVID-19 convalescent plasma donor candidates. J. Clin. Invest. 131, e144930 (2021).

Article  CAS  PubMed  Google Scholar 

Reiss, S. et al. Comparative analysis of activation induced marker (AIM) assays for sensitive identification of antigen-specific CD4 T cells. PLoS ONE 12, e0186998 (2017).

Article  PubMed Central  Google Scholar 

Glanville, J. et al. Identifying specificity groups in the T cell receptor repertoire. Nature 547, 94–98 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dash, P. et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 547, 89–93 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oberhardt, V. et al. Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine. Nature 597, 268–273 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Francis, J. M. et al. Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2. Sci. Immunol. 7, eabk3070 (2022).

CAS  PubMed  Google Scholar 

Shomuradova, A. S. et al. SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors. Immunity 53, 1245–1257 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Szeto, C. et al. Molecular basis of a dominant SARS-CoV-2 spike-derived epitope presented by HLA-A*02:01 recognised by a public TCR. Cells 10, 2646 (2021).

Article  CAS  PubMed Central  Google Scholar 

Ferretti, A. P. et al. Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2 that largely reside outside the spike protein. Immunity 53, 1095–1107 (2020).

Article  CAS  PubMed  Google Scholar 

Robins, H. S. et al. Overlap and effective size of the human CD8+ T cell receptor repertoire. Immunology 2, 47ra64 (2010).

Google Scholar 

Sethna, Z. et al. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. Bioinformatics 35, 2974–2981 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flament, H. et al. Outcome of SARS-CoV-2 infection is linked to MAIT cell activation and cytotoxicity. Nat. Immunol. 22, 322–335 (2021).

Article  CAS  Google Scholar 

Parrot, T. et al. MAIT cell activation and dynamics associated with COVID-19 disease severity. Sci. Immunol. 5, eabe1670 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Boulouis, C. et al. MAIT cell compartment characteristics are associated with the immune response magnitude to the BNT162b2 mRNA anti-SARS-CoV-2 vaccine. Mol. Med. 28, 54 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Le Gall, S., Stamegna, P. & Walker, B. D. Portable flanking sequences modulate CTL epitope processing. J. Clin. Invest. 117, 3563–3575 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Saggau, C. et al. The pre-exposure SARS-CoV-2-specific T cell repertoire determines the quality of the immune response to vaccination. Immunity 55, 1924–1939 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mudd, P. A. et al. SARS-CoV-2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans. Cell 185, 603–613 (2022).

Article  CAS  Google Scholar 

Pogorelyy, M. V. et al. Resolving SARS-CoV-2 CD4+ T cell specificity via reverse epitope discovery. Cell Rep. Med. 3, 100697 (2022).

Article  CAS