Identification and characterization of a SARS-CoV-2 specific CD8 T cell response with immunodominant features

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 COVID-19 patients 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 post recovery from critical and severe disease, and these responses convert from dysfunctional effector to functional memory CD8 T cells during convalescence. Single-cell RNA sequencing (incl. TCRseq) using the 10x Genomics Chromium system (5' kit) was performed on CD8 T cells from 6 COVID-19 patients with acute severe and critical disease. Bulk CD8 T cells were sorted from PBMCs and sequenced in two independent experiments (batch I and II). Patients were hashtagged (BioLegend TotalSeq-C anti-human hashtags) and pMHC monomers with indicated epitopes were conjugated to TotalSeq-C-conjugated-streptavidin. Barcode/hashtag assignments (batch I): Patient COVID-087 (Hashtag #1: GTCAACTCTTTAGCG); Epitopes: RLNEVAKNL-MHC (CGTATGCGCTTCAAG), YLQPRTFLL-MHC (CAGCAACTTCATTGT). Patient COVID-096 (Hashtag #3: TTCCGCCTCTCTTTG); Epitopes: PTDNYITTY-MHC (CAGCAACTTCATTGT), TTDPSFLGRY-MHC (GGTATAAGAGCTACG), TVATSRTLSY-MHC (ATGCGATCAGACCGA). Patient COVID-117 (Hashtag #4: AGTAAGTTCAGCGTA); Epitopes: TTDPSFLGRY-MHC (GGTATAAGAGCTACG). Patient COVID-143 (Hashtag #5: AAGTATCGTTTCGCA); Epitopes: CTDDNALAYY-MHC (ATGCGATCAGACCGA), DTDFVNEFY-MHC (CGTATGCGCTTCAAG), PTDNYITTY-MHC (CAGCAACTTCATTGT), TTDPSFLGRY-MHC (GGTATAAGAGCTACG). Patient COVID-153 (Hashtag #7: TGTCTTTCCTGCCAG); Epitopes: PTDNYITTY-MHC (CAGCAACTTCATTGT), TTDPSFLGRY-MHC (GGTATAAGAGCTACG). Barcode/hashtag assignments (batch II): Patient COVID-131 (Hashtag #1: GTCAACTCTTTAGCG), TTDPSFLGRY-MHC (ATGCGATCAGACCGA), VTEHDTLLY-MHC (CGTATGCGCTTCAAG), PTDNYITTY-MHC (CAGCAACTTCATTGT), FTSDYYQLY-MHC (GGTATAAGAGCTACG)