Enhanced Spike-specific, but attenuated Nucleocapsid-specific T cell responses upon SARS-CoV-2 breakthrough versus non-breakthrough infections

Abstract

SARS-CoV-2 vaccine breakthrough infections frequently occurred even before the emergence of Omicron variants. Yet, relatively little is known about the impact of vaccination on SARS-CoV-2-specific T cell and antibody response dynamics upon breakthrough infection. We have therefore studied the dynamics of CD4 and CD8 T cells targeting the vaccine-encoded Spike and the non-encoded Nucleocapsid antigens during breakthrough infections (BTI, n=24) and in unvaccinated control infections (non-BTI, n=30). Subjects with vaccine breakthrough infection had significantly higher CD4 and CD8 T cell responses targeting the vaccine-encoded Spike during the first and third/fourth week after PCR diagnosis compared to non-vaccinated controls, respectively. In contrast, CD4 T cells targeting the non-vaccine encoded Nucleocapsid antigen were of significantly lower magnitude in BTI as compared to non-BTI. Hence, previous vaccination was linked to enhanced T cell responses targeting the vaccine-encoded Spike antigen, while responses against the non-vaccine encoded Nucleocapsid antigen were significantly attenuated.

Keywords: COVID-19; SARS Cov 2; T cell response; adaptive immunity; breakthrough infection; vaccine.

Figure 1

Representative dot plots for detection of IFNy+ T cell targeting vaccine-encoded Spike and non-encoded Nucleocapsid protein. Representative dot plots from intracellular cytokine staining experiments gated on CD4+ (left plots) or CD8+ T cells (right plots) are shown for one breakthrough (BTI) and one non-breakthrough (non-BTI) infection case for peripheral blood mononuclear cells restimulated Spike and Nucleocapsid peptide pool as indicated. The red square indicates the gate for defining antigen-specific IFNy+ T cells within the CD4 or CD8 T cell parent population. The frequencies of IFNy+ T cells is indicated as percent of CD4 or CD8 T cells for each shopn gate. Dot plots were produced using FlowJo version 10.

Figure 2

T cell and binding antibody responses targeting vaccine-encoded Spike and non-encoded Nucleocapsid protein. The frequency of Spike-specific IFNy+ CD4+ (A) and CD8+ (B) and Nucleocapsid-specific IFNy+ CD4+ (C) and CD8+ (D) T cells and concentration of binding antibodies against the Spike-Receptor Binding Domain (RBD) (E) and Nucleocapsid (N) (F) in breakthrough infections (orange boxes) and non-breakthrough infections (blue boxes) are shown as median and quartiles enclosing 50% of the datapoints, whiskers extend up to the last point inside 1.5*(IQ3 - IQ1) range (Tukey definition). Specific T cell responses were detected after in vitro antigen-stimulation of freshly isolated PBMCs, while the specific antibody concentrations (Spike-RBD) or counts (Nucleocapsid) (Y-axis) consider all Ig isotypes and were determined using the Roche Elecsys test. The days since first diagnosis by PCR are indicated on the x-axis. Statistical comparisons between the groups were performed using the Mann-Whitney t test. p-values below 0.05 are indicated for figure 2 (A–F) Spike-RBD binding Ig concentrations significantly differed between the groups during all 5 weeks post infection.