CD8 Escape Muts Track Settings
T-Cell MHCI CD8+ Escape Mutations from Agerer et al. Sci Immun 2020   (All Immunology tracks)

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Assembly: SARS-CoV-2 Jan. 2020 (NC_045512.2)
Data last updated at UCSC: 2021-05-27 15:24:13


Cytotoxic T lymphocytes (CTL) find and kill cells infected with viruses by examining viral epitopes presented by MHC class I molecules on the surface of the cell. In the context of SARS-CoV-2, infected patients have elicited CTL responses by showing higher levels of granzyme B, perforin and IFN-gamma. Rapid rate of mutation in SARS-CoV-2 may hinder the presentation of peptides by MHC-I molecules thereby evading T cell response.

Agerer et al. performed deep sequencing of viral genomes from several patients and identified mutations that were observed in Nucleocapsid (N), ORF1ab, Membrane (M), and Envelope (E) proteins. This track includes 194 mutants spanning 305 T-cell epitopes restricted to HLA-A*02:01 and HLA-B*40:01.


In this study, deep sequencing was performed on virus samples from Austria. To identify mutant epitopes, MHC-I binding assays were performed. Subsequently, PBMCs collected from HLA-A*02:01 and HLA-B*40:01 typed, COVID-19 patients were subjected to functional assays. A more detailed description of the methodology is decribed in the original article.


Agerer B, Koblischke M, Gudipati V, Montaño-Gutierrez LF, Smyth M, Popa A, Genger JW, Endler L, Florian DM, Mühlgrabner V et al. SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses. Sci Immunol. 2021 Mar 4;6(57). PMID: 33664060