Research Article

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans

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Science  04 Aug 2020:
eabd3871
DOI: 10.1126/science.abd3871
  • Fig. 1 Characteristics of SARS-CoV-2 epitopes identified in unexposed donors.

    Reactivity was determined by FluoroSPOT assay after 17 days of in vitro stimulation of unexposed donor PBMCs (n=18) with one pool of peptides spanning the entire sequence of the spike protein (CD4-S), or a non-spike “megapool” (CD4-R) of predicted epitopes from the non-spike (i.e., “remainder”) regions of the viral genome. (A) Summary of the responses as a function of the protein of origin. (B) Spearman correlation of positive responses per SARS-CoV-2 protein size. (C) Percent similarity of the identified epitopes with common cold coronavirus peptides as a function of the number of responding donors. (D) Each dot shows the reactivity of a donor/epitope combination derived from either non-spike (CD4-R) or spike (CD4-S). Black bars indicate the geometric mean and geometric SD. Red indicates donor/epitope combinations with sequence identity >67% with common cold coronaviruses, while blue indicates highly reactive donor/epitopes combinations (>1000 SFC*106) with sequence identity ≤67%. In (C) and (D), statistical comparisons are performed by two-tail Mann-Whitney test. *** p<0.001, **** p<0.0001.

  • Fig. 2 CD4+ T cells in SARS-CoV-2-unexposed and COVID-19 individuals against HCoV epitopes homologous to SARS-CoV-2 epitopes.

    (A) Example of flow cytometry gating strategy for antigen-specific CD4+ T cells based on AIM (OX40+ and CD137+ double expression) after stimulation of PBMCs with HCoV or SARS-CoV-2 peptides. (B to D) Antigen-specific CD4+ T cells measured as a percentage of AIM+ (OX40+CD137+) CD4+ T cells after stimulation of PBMCs with HCoV epitopes homologous to SARS-CoV-2 epitopes. Samples were derived from SARS-CoV-2-unexposed donors (unexposed, n = 25) and recovered COVID-19 patients (COVID-19, n = 20). Black bars indicate the geometric mean and geometric SD. Each dot is representative of an individual subject. Statistical pairwise comparisons [(B) and (C)] were performed with the Wilcoxon test. P-values related to comparisons to the DMSO controls are listed at the bottom of the graphs, while any significant p-values related to inter-group comparisons are listed on top of the graphs. Statistical comparisons across cohorts were performed with the Mann-Whitney test (D). See also figs. S5 and S6.

  • Fig. 3 Phenotypes of antigen-specific CD4+ T cells from SARS-CoV-2-unexposed and COVID-19 responding to HCoV epitopes homologous to SARS-CoV-2 epitopes.

    (A) Example of flow cytometry gating strategy for antigen-specific CD4+ T cell subsets after overnight stimulation of PBMCs with HCoV or SARS-CoV-2 peptides ex vivo. (B and C) Phenotype of antigen-specific CD4+ T cells (OX40+CD137+) responding to indicated pools of SARS-CoV-2 and HCoV epitopes in unexposed and recovered COVID-19 patients. Data are shown as mean +/− SD. Each dot represents an individual subject. Statistical pairwise comparisons in (B) and (C) were performed with the Wilcoxon test. (D) Overall averages of antigen-specific CD4+ T cell subsets detected in unexposed and COVID-19 subjects. See also fig. S5.

  • Fig. 4 Cross-reactivity of SARS-CoV-2 and homologous HCoV peptides.

    Twelve short-term cell lines were generated using specific SARS-CoV-2 epitope/donor combinations selected on the basis of the primary screen. After 14 days of in vitro expansion, each T cell line was tested with the SARS-CoV-2 epitope used for stimulation and peptides corresponding to analogous sequences from other HCoVs at six different concentrations (1μg/mL, 0.1μg/mL, 0.01μg/mL, 0.001μg/mL, 0.0001μg/mL, 0.00001μg/mL). Spot forming cells per million (SFC/106) PBMCs are plotted for T cell lines stimulated with each peptide. See also fig. S7.

Supplementary Materials

  • Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans

    Jose Mateus, Alba Grifoni, Alison Tarke, John Sidney, Sydney I. Ramirez, Jennifer M. Dan, Zoe C. Burger, Stephen A. Rawlings, Davey M. Smith, Elizabeth Phillips, Simon Mallal, Marshall Lammers, Paul Rubiro, Lorenzo Quiambao, Aaron Sutherland, Esther Dawen Yu, Ricardo da Silva Antunes, Jason Greenbaum, April Frazier, Alena J. Markmann, Lakshmanane Premkumar, Aravinda de Silva, Bjoern Peters, Shane Crotty, Alessandro Sette, Daniela Weiskopf

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S8
    • Tables S1 to S8
    • References
    MDAR Reproducibility Checklist

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