CD4+ and CD8+ T cells and antibodies are associated with protection against Delta vaccine breakthrough infection: a nested case-control study within the PITCH study

Abstract

Defining correlates of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine breakthrough infection informs vaccine policy for booster doses and future vaccine designs. Existing studies demonstrate humoral correlates of protection, but the role of T cells in protection is still unclear. In this study, we explore antibody and T cell immune responses associated with protection against Delta variant vaccine breakthrough infection in a well-characterized cohort of UK Healthcare Workers (HCWs). We demonstrate evidence to support a role for CD4+ and CD8+ T cells as well as antibodies against Delta vaccine breakthrough infection. In addition, our results suggest a potential role for cross-reactive T cells in vaccine breakthrough.

Keywords: COVID vaccine; COVID-19; Delta; SARS-CoV-2; T cells; antibody; immunity; vaccine breakthrough.

Fig 1

Study design and comparison of antibody and T cell responses between cases and controls at 28 d after the second vaccine dose. (A) Schematic representation of study design including vaccination and breakthrough infection time points. Created using Biorender.com. (B) Venn diagram illustrating number of subjects with IgG and/or IFNγ ELISpot measurements, by case/control status. (C) Ancestral SARS-CoV-2 spike- (S), receptor binding domain- (RBD) and nucleoprotein- (N) specific IgG binding titer in cases and controls according to infection history, as measured by MSD. Naïve represents those with no history of prior infection (cases n = 26, controls n = 123). Convalescent (Conv) represents those with a history of infection prior to vaccination (cases n = 6, controls n = 77). All represents summation of Naïve and Conv participants (cases n = 32, controls n = 200). Dashed lines represent threshold for a positive response (SARS-CoV-2 S IgG 1160 AU/mL, RDB IgG 1169 AU/mL, and N IgG 3874 AU/mL). (D) Neutralizing antibody titers against ancestral (WT) and Delta (B1.617.2) isolates in a subset of cases (n = 21) and controls (n = 41) measured by live virus microneutralization (LV-MN) assay. Area between IC50 = 40 and IC50 = 2,560 (dashed black lines) corresponds to the quantitative range of the assay. IC50 = 5, IC50 = 10, and IC50 = 5,120 (solid gray lines) represent no, weak, and complete inhibition, respectively. (E) T cell responses to peptide pools representing ancestral SARS-CoV-2 S1, S2, total S (summation of S1 and S2 responses) and membrane (M) and N responses in cases and controls according to infection history, as measured by IFNγ ELISpot assay. Naïve cases n = 22, controls n = 114. Conv cases n = 2, controls n = 77. All cases n = 24, controls n = 191. Dashed lines represent threshold for a positive response [29 SFU/10⁶ peripheral blood mononuclear cells (PBMC)] calculated as mean background (DMSO) response +2 standard deviations. (F) Correlation between anti-S IgG titers, as measured by MSD, and total S T cell responses, as measured by IFNγ ELISpot, for all cases (n = 24) and controls (n = 144) where both parameters were measured. Dashed lines represent the median value for each parameter. (G) Frequency of individuals with vaccine breakthrough (VB) in each quadrant of the graph in (F). Individuals are classified as having “High” or “Low” IgG and IFNγ responses on the basis of whether their response is above or below the median for each variable. Number of cases and controls per group are shown below the graph. Values of 0 are replaced with 1 for representation on the logarithmic scale. Orange circles represent cases, and blue circles represent controls. Bars represent median of each group (C–E). Error bars represent interquartile range (C–E) or 95% CI (G). Two-tailed P values derived from Mann-Whitney U tests [comparing cases to controls or naïve to convalescent, (C–E)], Wilcoxon matched pairs signed rank tests [comparing WT and Delta responses, (D)] or pairwise Fisher’s exact tests (G) shown above linking lines. For clarity, only adjusted P values < 0.1 are shown in (G). Fold change in median response shown below linking lines or in brackets, calculated as median response for controls divided by median response for cases, median response for convalescent divided by median response for naïve, or median response for Delta divided by median response for WT.

Fig 2

Comparison of memory B cell and T cell responses in a subset of cases and matched controls at 28 d after the second vaccine dose. (A) Venn diagram illustrating the overlapping subsets of cases and controls analyzed in (B–D). (B) Memory B cell responses against ancestral (WT) and Delta (B.1.617.2; AY.1, AY.2, AY.3) SARS-CoV-2 spike (S) in a subset of cases (n = 10) and matched controls (n = 11) measured by memory B cell IgG FluoroSpot. (C) Proportion of cells expressing IFNγ, TNF, or IL-2 in response to peptide pools representing ancestral (WT) or Delta (B.1.617.2) S in the CD4+ T cell population and (D) CD8+ T cell population, in a subset of cases and matched controls (n = 12 per group), as measured by intracellular cytokine staining and flow cytometry. Populations were analyzed by gating on single, live, CD3+ cells. Orange circles represent cases, and blue circles represent controls. Bars represent the median of each group. Paired data from the same individual are linked by gray lines. Two-tailed P values derived from Mann-Whitney U tests (comparing cases to controls) or Wilcoxon matched pairs signed rank tests (comparing WT and Delta responses) are shown above linking lines. Fold change in median response shown in brackets for comparisons where P < 0.05, calculated as median response for controls divided by median response for cases, or median response for Delta divided by median response for WT.