207229f284b91ec0bd2eaa856fe639d7786fe8e9
max
  Mon Apr 27 12:26:51 2020 -0700
adding T cell epitopes track, refs #25458

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+<H2>Description</H2>
+<P>
+<p>This track shows data from  Braun et al, 2020,<a target=_blank href = "https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.full.pdf+html">"Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors"</a>
+<p>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."
+
+<h2>Display Conventions and Configuration</h2>
+<p> 
+Two tracks are available:
+</p>
+<ul>
+<li>M1_peptides: The more N-terminal peptide library
+<li>M2 peptides: The more C-terminal peptide library
+</ul>
+
+<p> The annotated interval represents the alignment of the peptide to the viral
+genome.  The sequence displayed in the name is SARS-CoV peptide sequence (which
+is the actual sequence which was used in the paper, but not necessarily
+identical to the SARS-CoV-2 peptide).</p>
+
+<h2>Methods</h2>
+<p>Table S1 contains the peptide sequences (SARS-CoV sequence) used.  This table was downloaded and tblastn was used to align the identified the SARS-CoV peptides to the SARS-CoV-2 genome.
+<p>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.
+<p>
+
+<h2>References</h2>
+Braun et al, 2020<a target=_blank href = "https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.full.pdf+html">"Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors"</a>