Replication Data for: Immunodominant T cell responses to SARS-CoV-2 nucleocapsid protein in Omicron breakthrough infection post-inactivated vaccination

The widespread administration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has not eliminated breakthrough infections due to immune evasion by viral mutations. Whether individuals with breakthrough infections can elicit effective T cell responses against the circulating Omicron JN.1 variant and the specific immunodominant characteristics of these responses, remain unclear. To address this, we recruited 57 individuals with breakthrough infections following a three-dose regimen of inactivated SARS-CoV-2 vaccines. Intracellular cytokine staining was used to evaluate T cell responses to the JN.1 nucleocapsid (N) protein overlapping peptide pool in peripheral blood mononuclear cells. Immunodominant epitopes were identified using a three-dimensional matrix screening approach. Truncated peptides stimulation assays and human leukocyte antigen (HLA) blocking assays were conducted to define the minimal epitope and HLA restriction of the dominant epitope. We found that Omicron breakthrough infections elicited robust CD4+ and CD8+ T cell responses, characterized by a Th1/Tc1-skewed phenotype and preserved polyfunctionality. The immunodominant epitope profile of the N protein shifted significantly with new epitopes targeting mutated sites emerged while previously dominant epitopes, such as N-4 and N-66, no longer maintained their immunodominance. Instead, epitope N-24 emerged as the most immunodominant target for CD4+ T cells, with minimal epitope length exceeding 13 amino acids and restricted by HLA-DR. Our finding demonstrates that Omicron breakthrough infections induce robust T cell responses targeting the circulating JN.1 strain and highlight the immunodominant features of these responses. These observations underscore the critical need to refine vaccine strategies in response to the dynamic evolution of viral variants.