Comprehensive longitudinal profiling identifies differential frequency, epitope specificity, and effector function of CD8+ T-cells across COVID-19 disease severities
eBioMedicine, 2026
Amaya Hernandez S., Munk K., Danilov K., Kadivar M., Hersby D., Tamhane T., Stegenborg-Grathwohl S., Pedersen A., Gang A., Hadrup S., Saini S.
| Disease area | Application area | Sample type | Products |
|---|---|---|---|
Infectious Diseases | Pathophysiology | Cell Culture Supernatant |  Olink Target 48 |
Abstract
Background
CD8+ T-cells are crucial for controlling and resolving SARS-CoV-2 infection, yet their epitope specificity and relationship to COVID-19 disease severity remain incompletely understood.
Methods
We performed comprehensive longitudinal profiling of antigen-specific CD8+ T-cell populations using DNA-barcoded peptide–HLA multimers, analysing 553 SARS-CoV-2 epitopes across globally prevalent HLA alleles in patients with mild and severe COVID-19. Functional and phenotypic characterisation was performed using multidimensional single-cell analysis and detailed cytokine profiling. The impact of post-infection COVID-19 vaccination on T-cell memory was also assessed.
Findings
Severe and mild COVID-19 were associated with robust yet distinct patterns of CD8+ T-cell activation. In the acute phase, severe disease was characterised by a broader T-cell repertoire (139 unique epitopes) with a median frequency of 1.4% (IQR 0.2–5.0) and a high-frequency of immunodominant epitope-specific T-cells that exhibited reduced cytotoxic profile. In contrast, patients with mild COVID-19 mounted responses against a more limited set of epitopes (98 unique epitopes), partially overlapping with those observed in severe disease, with a median T-cell frequency of 0.7% (IQR 0–1.9) and displayed a stronger cytotoxic phenotype and functional state. Over time, the memory T-cell compartment contracted to a restricted subset of immunodominant epitopes in the two patient groups and COVID-19 vaccination further enhanced frequencies of spike-specific T-cells independent of prior disease severity.
Interpretation
These findings delineate the epitope-specific frequency, function, and persistence of antigen-specific T-cell populations during SARS-CoV-2 infection, highlighting how differential activation, rather than magnitude alone, shapes immune outcomes across disease severities and other viral infections.