Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals

Abstract

The emergence of SARS-CoV-2 variants with evidence of antibody escape highlight the importance of addressing whether the total CD4⁺ and CD8⁺ T cell recognition is also affected. Here, we compare SARS-CoV-2-specific CD4⁺ and CD8⁺ T cells against the B.1.1.7, B.1.351, P.1, and CAL.20C lineages in COVID-19 convalescents and in recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. The total reactivity against SARS-CoV-2 variants is similar in terms of magnitude and frequency of response, with decreases in the 10%-22% range observed in some assay/VOC combinations. A total of 7% and 3% of previously identified CD4⁺ and CD8⁺ T cell epitopes, respectively, are affected by mutations in the various VOCs. Thus, the SARS-CoV-2 variants analyzed here do not significantly disrupt the total SARS-CoV-2 T cell reactivity; however, the decreases observed highlight the importance for active monitoring of T cell reactivity in the context of SARS-CoV-2 evolution.

Keywords: CD4; CD8; COVID-19; SARS-CoV-2; T cells; VOCs; vaccines.

Graphical abstract

Figure 1

T cell responses of COVID-19 convalescent individuals against ancestral and variant SARS-CoV-2 spike (S) PBMCs of COVID-19 convalescent individuals (n = 28) were stimulated with the S MPs corresponding to the ancestral reference strain (black) and the B.1.1.7 (gray), B.1.351 (red), P.1 (orange), and CAL.20C (light blue) SARS-CoV-2 variants. (A) The gating strategy for the AIM assay is illustrated by representative graphs defining S-specific CD4⁺ or CD8⁺ T cells by expression of OX40⁺CD137⁺ and CD69⁺CD137⁺, respectively. These graphs depict 1 of the COVID-19 convalescent donors from this study tested with the S MPs corresponding to each of the VOCs tested. (B) Percentages of AIM⁺ (OX40⁺CD137⁺) CD4⁺ T cells. (C) Percentages of AIM⁺ (CD69⁺CD137⁺) CD8⁺ T cells. (D) IFN-γ spot-forming cells (SFCs) per million PBMCs. (E) IL-5 SFCs per million PBMCs. (F and G) The data shown in (B) and (C) are plotted to show the titration of the S MPs (1 μg/mL, 0.1 μg/mL, and 0.01 μg/mL) for CD4⁺ (F) and CD8⁺ (G) T cells for each SARS-CoV-2 variant. The geometric mean of the 0.1 μg/mL condition is listed above each titration. Paired comparisons of ancestral S MPs versus each of the variants were performed by 1-tailed Wilcoxon test and are indicated by the p values in (B)–(D). In all of the panels, the bars represent the geometric mean. See also Figures S1, S2, S4, and S5 and Tables S1–S3.

Figure 2

T cell responses of COVID-19 convalescent individuals against ancestral and variant SARS-CoV-2 proteomes PBMCs of COVID-19 convalescent individuals (n = 28) were stimulated with MPs for the entire viral proteome corresponding to the ancestral reference strain (black) and the B.1.1.7 (gray), B.1.351 (red), P.1 (orange), and CAL.20C (light blue) SARS-CoV-2 variants. (A) Percentages of AIM⁺ (OX40⁺CD137⁺) CD4⁺ T cells for the total reactivity. (B) Percentages of AIM⁺ (CD69⁺CD137⁺) CD8⁺ T cells for the total reactivity. (C) Percentages of AIM⁺ (OX40⁺CD137⁺) CD4⁺ T cells for each MP. (D) Percentages of AIM⁺ (CD69⁺CD137⁺) CD8⁺ T cells for each MP. All of the bars represent the geometric mean. See also Figure S1, S2, S4, and S5 and Tables S1–S3.

Figure 3

T cell responses of COVID-19 vaccinees against ancestral and variant SARS-CoV-2 S PBMCs of Pfizer/BioNTech BNT162b2 (n = 14, triangles) and Moderna mRNA-1273 COVID-19 vaccinees (n = 15, circles) were stimulated with the S MPs corresponding to the ancestral reference strain (black) and the B.1.1.7 (gray), B.1.351 (red), P.1 (orange), and CAL.20C (light blue) SARS-CoV-2 variants. (A) The gating strategy for the AIM assay is illustrated by representative graphs defining S-specific CD4⁺ or CD8⁺ T cells by the expression of OX40⁺CD137⁺ and CD69⁺CD137⁺, respectively. These graphs depict one of the COVID-19 vaccinated donors from this study tested with the S MPs corresponding to each of the VOCs tested. (B) Percentages of AIM⁺ (OX40⁺CD137⁺) CD4⁺ T cells. (C) Percentages of AIM⁺ (CD69⁺CD137⁺) CD8⁺ T cells. (D) IFN-γ SFCs per million PBMCs. (E) IL-5 SFCs per million PBMCs. (F) Percentages of IFN-γ were calculated from the total IFN-γ and IL-5 SFCs per million PBMCs. (G and H) The data shown in (B) and (C) are also plotted showing the S MPs titration (1, 0.1, and 0.01 μg/mL) for CD4⁺ (G) and CD8⁺ (H) T cells with each SARS-CoV-2 variant. The geometric mean of the 0.1 μg/mL condition is listed above each titration. Paired comparisons of the ancestral reference strain-based S MP versus each of the variants were performed by one-tailed Wilcoxon test and are indicated by the p values in (B)–(D). In all of the panels, the bars represent the geometric mean. See also Figures S1 and S3–S5 and Tables S1–S3.

Figure 4

SARS-CoV-2 T cell epitope sequences affected by the variants CD4⁺ and CD8⁺ T cell epitopes of the ancestral strain identified in a previous study were analyzed as a function of the number and percentage of responses that are or are not conserved across the B.1.1.7 (gray), B.1.351 (red), P.1 (orange), and CAL.20C (light blue) SARS-CoV-2 variants. (A–D) The SARS-CoV-2 epitopes for the most immunodominant SARS-CoV-2 proteins in terms of numbers and percentage of response are shown for CD4⁺ (A and B) and CD8⁺ (C and D) T cells. (E–H) The SARS-CoV-2 epitopes for the S protein only in terms of numbers and percentage of response are shown for CD4⁺ (E and F) and CD8⁺ (G and H) T cells. (I–M) The peptide-binding algorithm data of mutated versus wild-type epitopes are shown for CD8⁺ (I–L) and for the effect of the mutations on CD8⁺ T cell epitopes, in which each instance was categorized as a function of whether the binding capability of the mutated peptide was increased (>2-fold), neutral, or decreased (<2-fold) (M). See also Table S4.