SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals

Abstract

Continuously emerging variants of concern (VOCs) sustain the SARS-CoV-2 pandemic. The SARS-CoV-2 Omicron/B.1.1.529 VOC harbours multiple mutations in the spike protein associated with high infectivity and efficient evasion from humoral immunity induced by previous infection or vaccination. By performing in-depth comparisons of the SARS-CoV-2-specific T-cell epitope repertoire after infection and messenger RNA vaccination, we demonstrate that spike-derived epitopes were not dominantly targeted in convalescent individuals compared to non-spike epitopes. In vaccinees, however, we detected a broader spike-specific T-cell response compared to convalescent individuals. Booster vaccination increased the breadth of the spike-specific T-cell response in convalescent individuals but not in vaccinees with complete initial vaccination. In convalescent individuals and vaccinees, the targeted T-cell epitopes were broadly conserved between wild-type SARS-CoV-2 variant B and Omicron/B.1.1.529. Hence, our data emphasize the relevance of vaccine-induced spike-specific CD8⁺ T-cell responses in combating VOCs including Omicron/B.1.1.529 and support the benefit of boosting convalescent individuals with mRNA vaccines.

Fig. 1. CD8⁺ and CD4⁺ T-cell responses targeting conserved and mutated epitopes in Omicron/B.1.1.529, BA.1.

a, Percentages of CD8⁺ T-cell responses to previously described optimal CD8⁺ T-cell epitopes within the complete WT SARS-CoV-2 variant B proteome normalized to the HLA allotype. b, Number and location of spike-specific CD8⁺ (top) and CD4⁺ (bottom) T-cell responses to OLPs of the spike protein detectable in SARS-CoV-2 convalescent individuals and vaccinees after two doses of Pfizer/BioNTech mRNA vaccine are depicted. The heatmaps depict the compiled data of tested individuals. Epitopes with amino acid sequence variations in Omicron/B.1.1.529, BA.1 are marked in red. The number of tested individuals (per HLA allotype and in total) and percentage of total T-cell responses targeting variant epitopes are indicated. WT: epitope conserved between WT SARS-CoV-2 variant B and Omicron/B.1.1.529; Mut: epitope mutated in Omicron/B.1.1.529 compared to WT variant B SARS-CoV-2. Source data

Fig. 2. Boosted vaccine- and infection-induced spike-specific CD8⁺ and CD4⁺ T-cell responses.

a,b, Number, location and percentages of spike-specific CD8⁺ and CD4⁺ T-cell responses to OLPs that are detectable in SARS-CoV-2 vaccinees after the second versus after the third dose of Pfizer/BioNTech mRNA vaccine (bnt162b2, measured 2–4 weeks after vaccination) (a) and in SARS-CoV-2 convalescent individuals who subsequently received a single dose of Pfizer/BioNTech mRNA boost vaccination (bnt162b2, measured 2 weeks after vaccination) (b). The heatmaps depict the data of one representative individual each. Targeted epitopes with sequence variations in Omicron/B.1.1.529, BA.1 are marked in red. c,d, Vaccinees and convalescent individuals with CD8⁺ (c) and CD4⁺ (d) T-cell responses within and outside highly conserved selective sweep regions in the spike protein are shown. Statistical analysis was performed with a two-sided Wilcoxon matched-pairs signed-rank test. Source data

Extended Data Fig. 1. CD8 + and CD4 + T cell responses targeting spike-specific epitopes.

(a) Intensity (sum interferon-γ production of all CD8 + T cell responses per patient) to optimal CD8 + T cell epitopes. (b) Number and location of spike-specific CD8 + and CD4 + T cell responses to overlapping peptides (OLP) in SARS-CoV-2 convalescents and vaccinees after two doses of Pfizer/BioNTech mRNA vaccine. Epitopes with amino acid sequence variations in omicron BA.2 are marked in blue. Number of CD8 + (c,e) and CD4 + (d,e) T cell responses targeting spike-specific epitopes per individual in convalescents (n = 19) and vaccinees after two doses of Pfizer/BioNTech mRNA vaccine (n = 16). Numbers of tested individuals (per HLA allotype and in total) and % of total T cell responses targeting variant epitopes are indicated. Median and range are depicted, statistical analysis was performed with two-sided Mann-Whitney-Test. NTD:N-Terminal Domain; RBD: receptor-binding domain; FCS: furin cleavage site; wt: epitope conserved between ancestral and omicron SARS-CoV-2; mut: epitope mutated in omicron compared to ancestral SARS-CoV-2. Source data

Extended Data Fig. 2. Stable T cell repertoire after infection and mRNA vaccination.

(a) Heatmaps showing percentage and location of CD4 + and CD8 + T cell responses targeting spike OLPs in three individuals at two different timepoints after mRNA vaccination. (b) Number of spike-specific CD4 + and CD8 + T cell responses to OLPs in correlation to days post symptoms onset in the first year after SARS-CoV-2 infection in the 19 convalescents. Spearman correlation analysis is depicted, p values are two-sided. Source data

Extended Data Fig. 3. Boosted vaccine- and infection-induced spike-specific CD8 + and CD4 + T cell responses in exemplary individuals.

Number, magnitude and location of spike-specific CD8 + and CD4 + T cell responses to overlapping peptides (OLP) that are detectable in (a) exemplary SARS-CoV-2 vaccinees after the 2^nd versus after the 3^rd dose of Pfizer/BioNTech mRNA vaccine (bnt162b2) and in (b) exemplary SARS-CoV-2 convalescents who subsequently received a single dose of Pfizer/BioNTech mRNA boost vaccination (bnt162b2) are depicted. Epitopes with amino acid sequence variations in omicron BA.1 are marked in red. Source data

Extended Data Fig. 4. Selective sweep regions.

(a) Schematic representation of four previously identified selective sweep regions (SS1-4) within the spike protein of SARS-CoV-2. (b) Amino acid sequences of the selective sweep regions 1-4 in the spike protein of ancestral SARS-CoV-2 and VOC alpha, beta, gamma, delta and omicron (including subvariant BA.1 and BA.2).

Extended Data Fig. 5. Gating strategy.

Lymphocytes were gated on FSC-A and SSC-A, Doublet exclusion on FSC-H and FSC-W, Exclusion of dead cells, Gating on CD8 + or CD4 + cells.