A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses

Abstract

While the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4⁺ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity.

Keywords: ADCC; COVID-19; SARS-CoV-2; T cell responses; coronavirus; humoral responses; mRNA vaccine; neutralization; spike glycoproteins; variants.

Graphical abstract

Figure 1

Elicitation of RBD- and spike-specific antibodies by a single dose of Pfizer/BioNTech mRNA vaccine in SARS-CoV-2 naive and previously infected individuals (A–D) Indirect ELISA was performed by incubating plasma samples from naive and PI donors collected before and after the first dose of vaccine with recombinant SARS-CoV-2 RBD protein. Anti-RBD Ab binding was detected using HRP-conjugated (A) anti-human IgM+IgG+IgA, (B) anti-human IgM, (C) anti-human IgA, or (D) anti-human IgG. Relative light unit (RLU) values obtained with BSA (negative control) were subtracted and further normalized to the signal obtained with the anti-RBD CR3022 mAb present in each plate. (E–H) Cell-based ELISA was performed by incubating plasma samples from naive and PI donors collected before and after the first dose of vaccination with HOS cells expressing full-length SARS-CoV-2 S. Anti-S Ab binding was detected using HRP-conjugated (E) anti-human IgM+IgG+IgA, (F) anti-human IgM, (G) anti-human IgA, or (H) anti-human IgG. RLU values obtained with parental HOS (negative control) were subtracted and further normalized to the signal obtained with the CR3022 mAb present in each plate. Limits of detection are plotted (^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001; ns, non-significant).

Figure 2

Detection of SARS-CoV-2 spike variants and other Betacoronaviruses (A–I) Cell-surface staining of 293T cells expressing full-length S from different SARS-CoV-2 variants and other human Betacoronavirus using plasma samples collected before and after first dose of vaccination in SARS-CoV-2 naive and PI donors. The graphs represent the median fluorescence intensities (MFIs) obtained. Limits of detection are plotted (^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001; ns, non-significant).

Figure 3

Neutralization and Fc-effector function activities in SARS-CoV-2 naive and previously infected individuals before and after a single dose of Pfizer/BioNTech mRNA vaccine (A) Neutralizing activity was measured by incubating pseudoviruses bearing SARS-CoV-2 S glycoproteins, with serial dilutions of plasma for 1 h at 37°C before infecting 293T-ACE2 cells. Neutralization half maximal inhibitory serum dilution (ID₅₀) values were determined using a normalized non-linear regression using GraphPad Prism software. (B) CEM.NKr parental cells were mixed at a 1:1 ratio with CEM.NKr-S cells and were used as target cells. PBMCs from uninfected donors were used as effector cells in a FACS-based ADCC assay. Limits of detection are plotted (^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001; ns, non-significant).

Figure 4

Spike-specific CD4⁺ and CD8⁺ T cell vaccine responses quantitatively and qualitatively differ in SARS-CoV-2 naive versus previously infected individuals (A–C) Net frequencies after S peptide pool stimulation of (A) total S-specific AIM⁺ CD4⁺ T cells, (B) S-specific AIM⁺ cTfh, (C) S-specific AIM⁺ CD8⁺ T cells in each donor prior to (V0) and post- (V1) vaccination in the SARS-CoV-2 naive participants and those with previous SARS-CoV-2 infection. (D and E) Net frequencies of total S-specific responses measured by ICS for (D) CD4⁺ and (E) CD8⁺ T cells for each donor prior to and post vaccination. ICS⁺ populations include cells that expressed at least one cytokine and effector function (CD40L, CD107a, IFN-γ, IL-2, IL-10, and TNF-α for CD4⁺; CD107a, IFN-γ, IL-2, IL-10, and TNF-α for CD8⁺ T cells). In (A–E), net frequency of the S-stimulated condition was calculated by subtracting the frequency detected in a DMSO control; bars correspond to median values, and symbols represent biologically independent samples from n = 24 SARS-CoV-2 naive individuals and n = 24 SARS-CoV-2 individuals with prior infection; lines connect data from the same donor. (F and G) Analysis of the polyfunctionality of S-specific (F) CD4⁺ and (G) CD8⁺ T cells measured by ICS at the post-vaccination (V1) time point. Data were analyzed by combinatorial gates based on the coexpression of CD40L, CD107a, IFN-γ, IL-2, IL-10, and TNF-α for CD4⁺ and CD107a, IFN-γ, IL-2, IL-10, and TNF-α for CD8⁺ T cells. Box-and-whisker plots show median values (line), 25^th to 75^th percentiles (box outline), and minimum and maximum values (whiskers). In (F and G), net frequency responses greater than 2-fold over DMSO control (background) were considered; significant p values were indicated by ^∗ for <0.05, ^∗∗ for <0.01, ^∗∗∗ for <0.001, and ∗∗∗∗ for <0.0001. P values were calculated by paired two-tailed Wilcoxon test for comparisons between the V0 and V1 time points in the same individual and Mann-Whitney for comparisons between the two cohorts at either the V0 or the V1 time point (A–E). Comparisons between the polyfunctionality patterns were calculated using Mann-Whitney test (F–G).

Figure 5

Total spike-specific CD4⁺ T cells and spike-specific cTfh responses at baseline correlate with humoral responses after vaccination (A) Heatmap showing associations between total S-specific CD4⁺ T cell or S-specific cTfh responses at baseline (V0) and Abs (against RBD and S), ADCC and neutralization functions after vaccination (V1). Color represents Rho value for each association calculated (Spearman correlation), and significant p values were indicated by ^∗ (^∗ for <0.05; ^∗∗ for <0.01, and ^∗∗∗ for <0.001). (B and E) Absence of significant correlations between IgM against S and AIM⁺ CD4⁺ T cells (B) and AIM⁺ cTfh responses (E). (C and F) Positive correlations between IgA against S and AIM⁺ CD4⁺ T cells (C) and AIM⁺ cTfh responses (F). (D and G) Positive correlation between IgG against S and AIM⁺ CD4⁺ T cells (D) and AIM⁺ cTfh responses (G). AIM⁺ cells were measured by flow cytometry and Abs were quantified by CBE. Each symbol identifies one donor (SARS-CoV-2 naive donors are represented by triangles and PI donors by circles).

Figure 6

Mesh of correlations of humoral and cellular parameters at discrete time points before and after vaccination in SARS-CoV-2 naive versus previously infected individuals Edge bundling correlation plots where red and blue edges represent positive and negative correlations between connected parameters, respectively. Only significant correlations (p < 0.05, Spearman rank test) are displayed. Nodes are color coded based on the grouping of parameters according to the legend. Node size corresponds to the degree of relatedness of correlations. Edge bundling plots are shown for correlation analyses using four different datasets; i.e., SARS-CoV-2 naive and PI individuals before and after vaccination, respectively.