Schema for CD8 Escape Muts - T-Cell MHCI CD8+ Escape Mutations from Agerer et al. Sci Immun 2020
  Database: wuhCor1    Primary Table: cd8escape Data last updated: 2021-05-27
Big Bed File: /gbdb/wuhCor1/cd8escape/cd8escape.bb
Item Count: 305
Format description: iedb bed9+ track
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart22366Start position in chromosome
chromEnd22393End position in chromosome
nameYLQPRTFLLName or ID of item, ideally both human readable and unique
score1000Score (0-1000)
strand++ or - for strand
thickStart22366Start of where display should be thick (start codon)
thickEnd22393End of where display should be thick (stop codon)
pom22393Point of mutation
geneSType of gene the peptide is originating from
pilnanProbable infection location
aa_changep.Leu277PheAmino acid change from wild-type to mutant
c_changettA/ttTCodon change from wild type to mutant
mutant_pepYLQPRTFLFMutant peptide

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndpomgenepilaa_changec_changemutant_pep
NC_045512v22236622393YLQPRTFLL1000+223662239322393Snanp.Leu277PhettA/ttTYLQPRTFLF
NC_045512v22236622393YLQPRTFLL1000+223662239322383Snanp.Thr274IleaCt/aTtYLQPRIFLL
NC_045512v22236622393YLQPRTFLL1000+223662239322370SIschgl, Landeck, Austriap.Leu270PheCtt/TttYFQPRTFLL
NC_045512v22271722747KLNDLCFTNV1000+227172274722736Snanp.Phe392LeuTtt/CttKLNDLCLTNV
NC_045512v22271722747KLNDLCFTNV1000+227172274722731Snanp.Leu390ProcTc/cCcKLNDPCFTNV
NC_045512v22271722747KLNDLCFTNV1000+227172274722737SMayrhofen, Schwaz, Austriap.Phe392SertTt/tCtKLNDLCSTNV
NC_045512v22271722747KLNDLCFTNV1000+227172274722740SMayrhofen, Schwaz, Austriap.Thr393IleaCt/aTtKLNDLCFINV
NC_045512v22271722747KLNDLCFTNV1000+227172274722746SNA, Wien-Land, Austriap.Val395AlagTc/gCcKLNDLCFTNA
NC_045512v22271722747KLNDLCFTNV1000+227172274722730SNA, Wien-Land, Austriap.Leu390PheCtc/TtcKLNDFCFTNV
NC_045512v22281022837KIADYNYKL1000+228102283722812Snanp.Lys417ArgaAg/aGgRIADYNYKL

CD8 Escape Muts (cd8escape) Track Description
 

Description

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.

Methods

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.

References

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