High‐resolution analysis of individual spike peptide‐specific CD4⁺ T‐cell responses in vaccine recipients and COVID‐19 patients

Abstract

Objectives Potential differences in the breadth, distribution and magnitude of CD4 + T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein between vaccinees, COVID‐19 patients and subjects who experienced both ways of immunisation have not been comprehensively compared on a peptide level. Methods Following virus‐specific in vitro cultivation, we determined the T‐cell responses directed against 253 individual overlapping 15‐mer peptides covering the entire SARS‐CoV‐2 spike glycoprotein using IFN‐γ ELISpot and intracellular cytokine staining. In vitro HLA binding was determined for selected peptides. Results We mapped 955 single peptide‐specific CD4 + T‐cell responses in a cohort of COVID‐19 patients ( n = 8), uninfected vaccinees ( n = 16) and individuals who experienced both infection and vaccination ( n = 11). Patients and vaccinees (two‐time and three‐time vaccinees alike) had a comparable number of CD4 + T‐cell responses (median 26 vs. 29, P = 0.7289). Most of these specificities were conserved in B.1.1.529 and the BA.4 and BA.5 sublineages. The highest magnitude of these in vitro IFN‐γ CD4 + T‐cell responses was observed in COVID‐19 patients (median 0.35%), and three‐time vaccinees showed a higher magnitude than two‐time vaccinees (median 0.091% vs. 0.175%, P < 0.0001). Twelve peptide specificities were each detected in at least 40% of subjects. In vitro HLA binding showed promiscuous presentation by DRB1 molecules for several peptides. Conclusion Both SARS‐CoV‐2 infection and vaccination prime broadly directed T‐cell responses directed against the SARS‐CoV‐2 spike glycoprotein. This comprehensive high‐resolution analysis of spike peptide specificities will be a useful resource for further investigation of spike‐specific T‐cell responses.

Post-pandemic memory T-cell response to SARS-CoV-2 is durable, broadly targeted and cross-reactive to hypermutated BA.2.86

“…We showed that non-spike T-cell responses constituted a sizable portion of the overall SARS-CoV-2 response, expanding the breadth of the response from vaccination. This was particularly striking for CD8 responses, with a third of responders targeting nucleocapsid and membrane in the absence of a CD8 spike response, consistent with epitope repertoires highly dependent on the HLA background of the individual 24,31 . Unlike the neutralization response, T cells targeting spike or non-spike antigens have the potential to clear infected cells and limit viral replication.…”

“…This is reassuring, given that the availability of updated booster vaccines based on XBB.1.5 in late 2023 30 is largely restricted to high income countries. The stable preservation of CD4 responses across variants suggests that most targeted epitopes are located in non-variable parts of spike or that mutations do not affect epitope recognition 31 . In contrast, as previously reported 6,9 , the preservation of CD8+ T-cell responses to variants is more heterogenous.…”

“…The stable preservation of CD4 responses across variants suggests that most targeted epitopes are located in non-variable parts of spike or that mutations do not affect epitope recognition 31 .…”

Single shot dendritic cell targeting SARS-CoV-2 vaccine candidate induces broad and durable systemic and mucosal immune responses

“…Since the Clec9A-targeting approach facilitates interaction of T cells with cDC1, coupled with the persistence of RBD-specific B cells, these conditions likely favor IL-27-mediated signaling, thereby promoting induction and maintenance of memory T cells. Furthermore, we observed that Clec9A-RBD immunization induced prominent CD8 + T cell responses despite the fact that SARS-CoV-2 RBD largely comprises of CD4 + T cell epitopes, and that RBD-specific cellular responses induced by existing COVID-19 vaccines are CD4 + dominated [50][51][52]. We previously showed that Clec9A targeting resulted in strong CD8 + T cell response owing to effective antigen cross-presentation activity in cDC1 [14,17].…”

“…Furthermore, we observed that Clec9A-RBD immunization induced prominent CD8 + T cell responses despite the fact that SARS-CoV-2 RBD largely comprises of CD4 + T cell epitopes, and that RBD-specific cellular responses induced by existing COVID-19 vaccines are CD4 + dominated [50-52]. We previously showed that Clec9A targeting resulted in strong CD8 + T cell response owing to effective antigen cross-presentation activity in cDC1 [14, 17].…”