Description

This track shows data from Braun et al, 2020, "Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors".

The authors stimulated PBMCs with two sets (M1 and M2) of overlapping SARS-CoV peptide pools. Importantly, these are SARS-CoV peptides that have experimental support as putative MHC-II epitopes for SARS-CoV, but note they do not all 100% match SARS-Cov-2 sequence.

Using these peptide sets, the authors "demonstrate the presence of S-reactive CD4+ 52 T cells in 83% of COVID-19 patients, 53 as well as in 34% of SARS-CoV-2 seronegative healthy donors (HD), albeit at lower frequencies."

Display Conventions and Configuration

Two tracks are available:

• M1_peptides: The more N-terminal peptide library
• M2 peptides: The more C-terminal peptide library

The annotated interval represents the alignment of the peptide to the viral genome. The sequence displayed in the name is the SARS-CoV peptide sequence (the actual sequence that was used in the paper, not necessarily identical to the SARS-CoV-2 peptide).

Methods

Table S1 contains the peptide sequences (SARS-CoV sequence) used. This table was downloaded and tblastn was used to align the identified SARS-CoV peptides to the SARS-CoV-2 genome.

A small number of peptides were not found or reported erroneous hits, in which the coordinates were identified by manually blat-ing the SARS-CoV-2 sequence from the alignments reported in Fig S1.

References