The COVID-19 pandemic caused by SARS-CoV-2 is a continuous challenge worldwide, and there is an urgent need to map the landscape of immunogenic and immunodominant epitopes recognized by CD8+ T cells. Here, we analyze samples from 31 patients with COVID-19 for CD8+ T cell recognition of 500 peptide-HLA class I complexes, restricted by 10 common HLA alleles. We identify 18 CD8+ T cell recognized SARS-CoV-2 epitopes, including an epitope with immunodominant features derived from ORF1ab and restricted by HLA-A*01:01. In-depth characterization of SARS-CoV-2-specific CD8+ T cell responses of patients with acute critical and severe disease reveals high expression of NKG2A, lack of cytokine production and a gene expression profile inhibiting T cell re-activation and migration while sustaining survival. SARS-CoV-2-specific CD8+ T cell responses are detectable up to 5 months after recovery from critical and severe disease, and these responses convert from dysfunctional effector to functional memory CD8+ T cells during convalescence.

A large global effort is currently ongoing to develop vaccines against SARS-CoV-2, the causative agent of COVID-19. While there is accumulating evidence on the antibody response against SARS-CoV-2, little is known about the SARS-CoV-2 antigens that are targeted by CD8 T cells. To address this issue, we have analyzed samples from 20 COVID-19 patients for T cell recognition of 500 predicted MHC class I epitopes. CD8 T cell reactivity against SARS-CoV- 2 was common. Remarkably, a substantial fraction of the observed CD8 T cell responses were directed towards the ORF1ab polyprotein 1ab, and these CD8 T cell responses were frequently of a very high magnitude. The fact that a major part of the SARS-CoV-2 specific CD8 T cell response is directed against a part of the viral genome that is not included in the majority of vaccine candidates currently in development may potentially influence their clinical activity and toxicity profile.

Global efforts are ongoing to develop vaccines against SARS-CoV-2 causing COVID-19. While there is accumulating information on antibody responses against SARS-CoV-2, less is known about CD8 T-cell recognized SARS-CoV-2 epitopes and the functional state of SARS- CoV-2-specific CD8 T cells. To address these issues, we analyzed samples from 18 COVID- 19 patients for CD8 T-cell recognition of 500 peptide HLA class I complexes, restricted by 10 common HLA alleles. Several epitopes derived from ORF1ab were identified, including an immunodominant epitope restricted by HLA-A*01:01. The immunodominance was further supported by high TCR diversity within the CD8 T cells specific for this epitope. Noteworthy, the ORF1ab is not included in the majority of vaccine candidates in development, which may influence their clinical activity. In-depth characterization of identified SARS-CoV-2-specific CD8 T cell responses revealed a lack of cytokine production and a gene expression profile inhibiting T cell re-activation and migration while sustaining cell survival.

A single model system for integrative studies on multiple facets of antigen presentation is lacking. PAKC is a novel panel of ten cell lines knocked out for individual components of the HLA class I antigen presentation pathway. PAKC will accelerate HLA‐I research in the fields of oncology, infectiology, and autoimmunity.