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."
Two tracks are available:
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).
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.