Background:
Characterization of long-term T-cell immunity against SARS-CoV-2 proteome is critical for understanding the implications of virus-specific hybrid immunity in protecting against re-infection and advancing novel vaccine designs. Here, we conducted a high-resolution mapping of the breadth and magnitude of T-cell responses to the entire SARS-CoV-2 proteome over a 2-year follow-up period in individuals with hybrid immunity.
Methods:
We selected cryopreserved PBMC from 38 healthcare workers, including 19 SARS-CoV-2 infected (CoV2+, tested at 124 days from symptoms onset, DfSO) and 19 uninfected (CoV2-) participants in the ProHEpiC-19 cohort study (NCT04885478). Longitudinal PBMC were available from 18 individuals after a 3-dose mRNA vaccination, including 13 CoV2+ (CoV2+Vac+, 825 DfSO) and 5 CoV2- who became infected during the follow-up period (Vac+CoV2+, 302 DfSO). We measured the breadth and magnitude of IFN-y T-cell responses by ELISpot assay using a 15-mer overlapping peptide (OLP) library of 2,790 SARS-CoV-2 peptides in 100 pools using a Mega Matrix approach, and we deconvoluted the matrix using single peptides by ELISpot assay.
Results:
We identified immunodominant T-cell responses to 13 regions across the SARS-CoV-2 proteome within S, Nsp3, NC, Env, and M proteins across groups and time. In addition, we observed a booster vaccination effect in these immunodominant regions with the strongest responses targeting S and Nsp3 proteins. In addition, CoV2+Vac+ individuals had broader T-cell responses than Vac+CoV2+ and showed an exclusive targeting of ORF3a, M, upORFs, Nsp2, 3C_LP, Nsp10 and Hel regions across the SARS-CoV-2 proteome. At the single peptide level, we identified differential frequency in the optimal T-cell responses across groups as the CoV2+Vac+ showed a preferential targeting of S1 (58%), S2 (17%) and ORF1ab/8 (25%) compared to Vac+CoV2+ with almost exclusive recognition of S2 (86%).
Conclusions:
Our results define immunodominant long-term T-cell responses in S, Nsp3, NC, Env, and M proteins in SARS-CoV2 proteome in the context of hybrid immunity. Our data demonstrate broader and exclusive T-cell responses in CoV2+Vac+ individuals compared to Vac+CoV2+. Overall, we identify differences in long-term T-cell hybrid immunity primed by infection or vaccination with implications for protection from re-infection and future vaccine design.