Science Immunology

The PDF file includes:

  • Fig. S1. Details of SARS-CoV-2 derived peptides in relation to their HLA and patient-specific coverage and immunogenicity.
  • Fig. S2. Examples of genome-wide screening for SARS-CoV-2-reactive T cells in individual COVID 19 patient samples.
  • Fig. S3. Summary of SARS-CoV-2-specific T cell reactivity identified in healthy donors.
  • Fig. S4. Representative flow cytometry plots of SARS-CoV-2-specific T cell multimer recognition in healthy donors.
  • Fig. S5. Gating strategy and functional evaluation of SARS-CoV-2-reactive CD8+ T cells identified in healthy donors.
  • Fig. S6. UMAP visualization comparing phenotype characteristics of SARS-CoV-2 peptide reactive T cells in the COVID 19 patient and healthy donor cohorts.
  • Fig. S7. Memory phenotype of SARS-CoV-2-reactive CD8+ T cells.
  • Fig. S8. Phenotype comparison of CEF- and SARS-CoV-2-specific T cell responses.
  • Fig. S9. Phenotype and functional evaluation of the immunodominant epitopes in hospitalized and outpatients.
  • Fig. S10. Sequence similarities of SARS-CoV-2 peptides with HCoV.
  • Fig. S11. Gating strategy for sorting multimer+ CD8+ T cells and phenotype analysis.
  • Table S2. COVID-19 patient information.
  • Table S6. Functional analysis of SARS-CoV-2 antigen-specific T cells in COVID-19 patients.
  • Table S8. Phenotype flow cytometry antibody panel.
  • Table S9. SARS-CoV-2 T cell epitopes with comparison to previously reported epitopes.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1. List of SARS-CoV-2 peptides analyzed for T cell reactivity with their HLA rank score (Excel file).
  • Table S3. CEF epitope library (Excel file).
  • Table S4. SARS-CoV-2 -specific T cell epitopes identified in COVID-19 patients (Excel file).
  • Table S5. CEF-specific T cell responses identified in COVID-19 patients, in pre-COVID-19 healthy donors (HD-1) and in high-risk healthy donors (HD-2) (Excel file).
  • Table S7. SARS-CoV-2 -specific T cell epitopes identified in pre-COVID-19 healthy donors (HD-1) and high-risk healthy donors (HD-2) (Excel file).
  • Table S10. HLA genotype data for patient and healthy donors (Excel file).
  • Table S11. Raw data file (Excel file).