Figure 1

SARS-CoV-2 mRNA vaccine induced memory T cells against wild-type and Omicron spike proteins. Peripheral blood samples were obtained before (T0), 1 week (T1), 2 months (T2), and 6 months (T3) after the 2nd dose of the BNT162b2 mRNA vaccine and 2 months after the 3rd dose (B-T2). (a) The timeline of vaccinations and sample collections is shown. (b–g) Activation-induced marker (AIM) assays were performed using peripheral blood mononuclear cells (PBMCs) obtained at the indicated time points. PBMCs were stimulated with peptide pools of SARS-CoV-2 structural proteins, including the spike and nucleocapsid, cytomegalovirus pp65 protein as a control (b–e), and a mutant pool of the spike protein of the SARS-CoV-2 Omicron variant (MP) and wild-type reference pool (WT) (f, g). Twenty-two hours later, T cells responding to the indicated peptide pools were identified as AIM⁺ (OX40⁺ CD137⁺) CD4⁺ T cells and AIM⁺ (CD69⁺ CD137⁺) CD8⁺ T cells by flow cytometry. Frequencies of AIM⁺ CD4⁺ T and AIM⁺ CD8⁺ T cells at each time point (b) and at T2, T3, and B-T2 (c) are shown. (d) Heatmaps show the correlations among S1-reactive AIM⁺ CD4⁺ T cell frequencies (left) and S1-reactive AIM⁺ CD8⁺ T cell frequencies (right) at the indicated time points. (e) Correlation between the frequencies of S1-reactive AIM⁺ CD4⁺ T cells at T1 and S1-reactive AIM⁺ CD8⁺ T cells at B-T2. (f) Frequencies of AIM⁺ CD4⁺ T and AIM⁺ CD8⁺ T cells reactive to MP and WT pools at B-T2. (g) Correlations between MP- and WT-reactive AIM⁺ CD4⁺ T cells and AIM⁺ CD8⁺ T cells at B-T2. CMV, cytomegalovirus pp 65 protein; N, SARS-CoV-2 nucleocapsid; S1, SARS-CoV-2 spike S1 domain; S mix, a mixture of SARS-CoV-2 spike S1 and S2 domains. Each dot indicates the value for one individual. Significant differences were analyzed by the Friedman test (b, c) and Wilcoxon matched-pairs signed-rank test (f). Correlations were analyzed using Spearman’s correlation analysis (e, g). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.