Broadly directed SARS-CoV-2-specific CD4+ T cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19

PLoS Pathog. 2021 Sep 16;17(9):e1009842. doi: 10.1371/journal.ppat.1009842. eCollection 2021 Sep.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acute Disease
  • Adult
  • Aged
  • CD4-Positive T-Lymphocytes / immunology*
  • COVID-19 / immunology*
  • Cohort Studies
  • Coronavirus Envelope Proteins / immunology
  • Coronavirus Nucleocapsid Proteins / immunology
  • Enzyme-Linked Immunospot Assay
  • Epitopes, T-Lymphocyte / immunology
  • Female
  • Humans
  • Male
  • Middle Aged
  • Phosphoproteins / immunology
  • SARS-CoV-2 / immunology*
  • Spike Glycoprotein, Coronavirus / immunology
  • Survivors
  • T-Cell Antigen Receptor Specificity
  • Viral Matrix Proteins / immunology

Substances

  • Coronavirus Envelope Proteins
  • Coronavirus Nucleocapsid Proteins
  • Epitopes, T-Lymphocyte
  • Phosphoproteins
  • Spike Glycoprotein, Coronavirus
  • Viral Matrix Proteins
  • envelope protein, SARS-CoV-2
  • membrane protein, SARS-CoV-2
  • nucleocapsid phosphoprotein, SARS-CoV-2
  • spike protein, SARS-CoV-2