f75874a85e09a19a652ca8c06cd72be5fba5482f
angie
  Thu Nov 12 08:59:08 2020 -0800
Added section about hgPhyloPlace/UShER to CoViD-19 landing page.  refs #26516

diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html
index aff5194..75ca004 100755
--- src/hg/htdocs/covid19.html
+++ src/hg/htdocs/covid19.html
@@ -93,30 +93,79 @@
               target="_blank">COVID-19 Airways</a>
               <li><a href="https://covid19-influenza-response.cells.ucsc.edu"
               target="_blank">COVID-19 and Influenza Immunophenotyping</a>
               <li><a href="https://covid19atlas.cells.ucsc.edu" target="_blank">COVID-19 Cell Atlas</a>
               <li><a href="https://scarface.cells.ucsc.edu"
               target="_blank">COVID-19 SARS-CoV-2 and coronavirus-associated
               receptors and factors (SCARFs)</a>
               <li><a href="https://hca-lungmap-integrated.cells.ucsc.edu"
               target="_blank">HCA-LungMAP COVID-19 Integrated Analysis</a>
             </ul>
             <p><a href="https://cells.ucsc.edu/?bp=lung"
             target="blank">Other Lung datasets in the Cell Browser</a>
     </div>
 </div>
 
+<div class="row">
+<a name="usher"></a>
+    <div class="col-md-12">
+      <h2>UShER for real-time genomic contact tracing</h2>
+    </div>
+    <div class="col-md-6">
+      <p>
+        <img align="left" alt="UShER logo"
+             src="/images/covid19/usher_logo.png"
+             style="border: none; width: 12em;">
+        In addition to the Genome Browser, we offer a
+        <a href="/cgi-bin/hgPhyloPlace" target=_blank>web interface</a> to
+        <a href="https://github.com/yatisht/usher" target=_blank>Ultrafast Sample placement
+          on Existing tRees (UShER)</a>
+        <a href="https://www.biorxiv.org/content/10.1101/2020.09.26.314971v1"
+           target=_blank>(Turakhia et al.)</a>,
+        a tool for identifying the relationships among a user's newly sequenced viral genomes
+        and all known SARS-CoV-2 virus genomes. UShER identifies relationships between viral
+        genomes by adding them to an existing phylogenetic tree of similar sequences that
+        visually depicts the evolutionary relationships among the genome sequences.
+        This approach empowers &quot;genomic contact tracing&quot;.
+        That is, UShER tells you whether virus genomes are closely related and therefore
+        possibly from the same source, or if they are distantly related and the infections
+        come from distinct sources.
+        When newly sequenced virus genomes are added to a comprehensive tree of previously
+        sequenced genomes, contact tracers are often able to determine where in the world
+        those genomes came from.
+        UShER is the only available method that can do this in &quot;real time&quot;.
+        Our tool places genomes onto a comprehensive global phylogeny of more than 80,000
+        virus genomes in less than one second.
+      </p>
+    </div>
+    <div class="col-md-6">
+        <a href="/images/covid19/UShER_example.png">
+        <img class="text-center" alt="Example output of UShER"
+            src="/images/covid19/UShER_example.png"
+                style="margin-bottom: 5px !important">
+        </a>
+        <div style="text-align: right; line-height: 1">
+          <font SIZE=-1><em>Example UShER results displayed using
+            <a href="https://nextstrain.org/" target=_blank>Nextstrain</a>.
+            Sequences representing a hypothetical outbreak are yellow;
+            previously sampled sequences are blue.  Branches are labeled
+            by nucleotide mutations.</em><BR>
+          </font>
+        </div>
+    </div>
+</div>
+
 <h2 id="news">News</h2>
 <ul>
 <li>
 <b>October 21, 2020</b>:
 <a target="_blank" href="goldenPath/newsarch.html#102120">
 New gene models, immunology, pathogenicity, and conservation annotation tracks</a>
 have been released. Click the above link to directly access track description pages
 for specific track titles such as PhyloCSF Genes, Weizman ORFs, icSHAPE RNA Structure,
 Validated epitopes from IEDB, and various Phylogenetic Tree tracks.
 </li>
 <li id="covidHgiGwas">
 <b>September 22, 2020</b>: 
 First COVID-19-related annotation track on UCSC human genome browser: 
 <a href="/cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas" target="_blank">
 COVID-19 GWAS</a>: GWAS meta-analyses of studies contributed by multiple partners world-wide (18 in