Figure 2.

Phenotypic Characteristics of SARS-CoV-2-Specific T Cells in Acute and Convalescent COVID-19

(A and B) Dot plots summarizing the expression frequencies of activation/cycling markers among tetramer⁺ CMV-specific (A) or EBV-specific CD8⁺ T cells (B) by group. Each dot represents one specificity in one donor. Data are shown as median ± IQR. ^∗p < 0.05, ^∗∗p < 0.01. Kruskal-Wallis rank-sum test with Dunn’s post hoc test for multiple comparisons.

(C) Representative flow cytometry plots (left) and bar graphs (right) showing the expression of activation/cycling markers among CD107a⁺ and/or IFN-γ⁺ SARS-CoV-2-specific CD4⁺ and CD8⁺ T cells (n = 6 donors). Numbers indicate percentages in the drawn gates. Data are shown as median ± IQR. NC, negative control. ^∗p < 0.05, ^∗∗p < 0.01. Paired t test or Wilcoxon signed-rank test.

(D) Representative flow cytometry plots (left) and bar graph (right) showing the upregulation of CD69 and 4-1BB (AIM assay) among CD38⁺ PD-1⁺ SARS-CoV-2-specific CD8⁺ T cells (n = 6 donors). Numbers indicate percentages in the drawn gates. S, spike; M, membrane; N, nucleocapsid.

(E) Left: representative flow cytometry plots showing the expression of activation/cycling markers among tetramer⁺ SARS-CoV-2-specific CD8⁺ T cells by group (red) and by total frequency (black). Center: UMAP plot showing the clustering of memory CD8⁺ T cells. Right: UMAP plots showing the clustering of tetramer⁺ SARS-CoV-2-specific CD8⁺ T cells by group and the expression of individual markers (n = 2 donors).

(F) Dot plots summarizing the expression frequencies of all quantified markers among tetramer⁺ SARS-CoV-2-specific CD8⁺ T cells by group. Each dot represents combined specificities in one donor. Data are shown as median ± IQR.

(G) Bivariate plots showing the pairwise correlations between symptom-free days and the expression frequencies of CCR7, CD45RA, or granzyme B (GzmB). Each dot represents combined specificities in one donor. Key as in (F). Spearman rank correlation.