Comprehensive longitudinal profiling of SARS-CoV-2 antigens reveals COVID-19 severity-associated CD8+ T-cell activation and functional impairment 3496

Abstract Description CD8+ T-cells are crucial for resolving SARS-CoV-2 infection. However, the persistence of SARS-CoV-2 epitope-specific CD8+ T-cell responses post-infection and their impact on COVID-19 pathogenesis remain unclear due to limited epitope-specific resolution. Using DNA-barcoded peptide-major histocompatibility complex (pMHC) multimers, we profiled CD8+ T-cell dynamics in severe and mild COVID-19 through a longitudinal analysis of 553 SARS-CoV-2 epitopes up to six months post-infection. In the acute phase, a large number of antigens (n = 199) contributed to CD8+ T-cell responses, while long-term memory formed towards a smaller antigen pool. Severe COVID-19 patients exhibited higher T-cell frequencies, primarily in HLA-A01:01-restricted responses, with an effector memory phenotype; however, despite the comparatively low frequency, T-cells in mild patients showed more cytotoxic terminally differentiated cells. Single-cell analysis revealed functionally impaired T-cells with low cytotoxicity and IFN-I signaling in severe cases, while mild patients had higher expression of cytotoxicity-associated genes (PRF1, GZMH, GZMB, GNLY). Importantly, the ORF1-derived HLA-A*01:01 restricted immunodominant epitope TTDPSFLGRY was found associated with increased T-cell frequency and the observed functional deregulation exclusively in severe COVID-19 patients. This study contributes to our understanding of the kinetics and durability of CD8+ T-cell responses and their role in COVID-19 severity. Funding Sources Grants: - REACT- Horizon Europe - Grant agreement No 101057129 - DFF Sapere Aude Topic Categories Viral Immunology (VIR)