Abstract
The aim of this study was to define the breadth and specificity of dominant SARS-CoV-2-specific T cell epitopes using a comprehensive set of 135 overlapping 15-mer peptides covering the SARS-CoV-2 envelope (E), membrane (M) and nucleoprotein (N) in a cohort of 34 individuals with acute (n = 10) and resolved (n = 24) COVID-19. Following short-term virus-specific in vitro cultivation, the single peptide-specific CD4+ T cell response of each patient was screened using enzyme linked immuno spot assay (ELISpot) and confirmed by single-peptide intracellular cytokine staining (ICS) for interferon-γ (IFN-γ) production. 97% (n = 33) of patients elicited one or more N, M or E-specific CD4+ T cell responses and each patient targeted on average 21.7 (range 0-79) peptide specificities. Overall, we identified 10 N, M or E-specific peptides that showed a response frequency of more than 36% and five of them showed high binding affinity to multiple HLA class II binders in subsequent in vitro HLA binding assays. Three peptides elicited CD4+ T cell responses in more than 55% of all patients, namely Mem_P30 (aa146-160), Mem_P36 (aa176-190), both located within the M protein, and Ncl_P18 (aa86-100) located within the N protein. These peptides were further defined in terms of length and HLA restriction. Based on this epitope and restriction data we developed a novel DRB*11 tetramer (Mem_aa145-164) and examined the ex vivo phenotype of SARS-CoV-2-specific CD4+ T cells in one patient. This detailed characterization of single T cell peptide responses demonstrates that SARS-CoV-2 infection universally primes a broad T cell response directed against multiple specificities located within the N, M and E structural protein.
Highlights
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a severe flu-like illness which is associated with hyperinflammation and immune dysfunction
This current study was designed to get a detailed understanding of the breadth and specificity of the CD4+ T cell response directed against the other structural proteins, namely the envelope (E), membrane (M) and nucleoprotein (N) using a comprehensive overlapping peptide set in a cohort of patients during early and resolved COVID-19
Three peptides elicited CD4+ T cell responses in more than 55% of all patients, two located within the M protein, and one located within the N protein
Summary
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a severe flu-like illness which is associated with hyperinflammation and immune dysfunction. The S protein is 1273 amino acids, the M protein 222 amino acids, and the E protein 75 amino acids long Together, these three antigens are part of the viral coat. The M protein is the most abundant structural protein and it defines the shape of the viral envelope [4]. It has a small N-terminal glycosylated ectodomain, three transmembrane domains, and a much larger C-terminal endodomain that extends 6–8 nm into the viral particle [4]. The E protein is the smallest of the four structural proteins This transmembrane protein has an N-terminal ectodomain and a C-terminal endodomain with ion channel activity, which is associated with pathogenesis [6]
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