697cd77a0d73699bc7326ed78c2679b759c910ae kate Wed Sep 23 16:34:43 2020 -0700 Add Max's intro about viral phylogenomics. And mention human browser COVID-related tracks (COVID-19 GWAS). refs #25217 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index e0a96c8..5239d54 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,48 +1,58 @@ <!DOCTYPE html> <!--#set var="TITLE" value="COVID-19 Resources at UCSC" --> <!--#set var="ROOT" value="." --> <!--#include virtual="$ROOT/inc/gbPageStart.html"--> <h1>COVID-19 Pandemic Resources at UCSC <span> <font size=-1 style="padding-left: 10px; padding-right: 10px; margin-left: 15px;"> -<a href="#news">Updated: September 22, 2020</a></font></span></h1> +<a href="#news">Updated: September 23, 2020</a></font></span></h1> <div class="row"> <div class="col-md-6"> <p> The SARS-CoV-2 coronavirus emerged in December 2019 as a novel human pathogen causing a severe acute respiratory syndrome (COVID-19). In the following months, the disease spread internationally and was <A TARGET="_BLANK" HREF="https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020"> declared a pandemic by the World Health Organization</a> on March 11, 2020. </p> - +<p> +Genome sequencing of the SARS-CoV-2 coronavirus has helped researchers study mechanisms of +transmission and infection and the reaction of the human immune system. Compared to other RNA viruses, the genome mutates little, but enough variants are known to determine how samples cluster into +groups and how they are related (as illustrated by the accompanying COVID-19 transmission map). +COVID-19 related datasets in the human genome are also beginning to become publicly available in +sufficient volume to merit meta-analysis and summarization, and can shed light on, for example, +genetic influences on infection susceptibility, disease severity, and outcomes. +</p> <p> We at the <a target="_blank" href="https://ucscgenomics.soe.ucsc.edu/">UC Santa Cruz Genomics Institute</a> are responding to the urgency of supporting biomedical research aimed at -developing therapeutics and a vaccine for this devastating illness by fast-tracking the -<a target="_blank" href="../cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a> -and incorporating relevant biomedical datasets such as single-cell lung gene expression into the -<a target="_blank" href="../singlecell.html">UCSC Cell Browser</a>. +developing therapeutics and a vaccine for this devastating illness by fast-tracking our +visualization of the SARS-CoV-2 genome sequences and analyses, the +<a target="_blank" href="../cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a>, +by incorporating relevant biomedical datasets such as single-cell lung gene expression into the +<a target="_blank" href="../singlecell.html">UCSC Cell Browser</a>, and by creating data tracks +of +<a target="_blank" href="#covidHgiGwas">COVID-19 annotations in our Human Genome Browsers</a>. </p> <p> -A manuscript describing this work, +A manuscript describing <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank"> The UCSC SARS-CoV-2 Genome Browser</a>, was published in the September 9 issue of <em>Nature Genetics</em>. </p> </div> <div class="col-md-6"> <img class="text-center" alt="COVID-19 transmission as of May 30, 2020, from Nextstrain" src="../images/covid19/covid19-transmission.may30_2020.nextstrain.png" style="margin-bottom: 5px !important"> <div style="text-align: right; line-height: 1"> <font SIZE=-1><em>COVID-19 transmission as of May 30, 2020</em><BR> </font> <font SIZE=-2> <A HREF="https://nextstrain.org" TARGET=_blank>Latest situation report from Nextstrain.org</a> @@ -83,33 +93,42 @@ 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> <h2 id="news">News</h2> <ul> +<li id="covidHgiGwas"> +<b>September 22, 2020</b>: +First COVID-19-related annotation track on UCSC human genome browser: +<a href="http://genome.ucsc.edu/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 +this release), as part of the +<a target="_blank" href="https://www.covid19hg.org">COVID-19 Host Genetics Initiative</a>, +a collaborative effort to facilitate the generation, analysis and sharing of COVID-19 host genetics research. +</li> <li> <b>September 9, 2020</b>: -The manuscript describing this work, +The manuscript describing the <a href="https://www.nature.com/articles/s41588-020-0700-8" target="_blank"> The UCSC SARS-CoV-2 Genome Browser</a>, is now published in <em>Nature Genetics</em>. </li> <li> <b>August 7, 2020</b>: <a target="_blank" href="https://genome.ucsc.edu/goldenPath/newsarch.html#080720"> Eight new annotation tracks</a>, presenting information about duplication regions, sequencing, gene identities, plasmid constructs, protein contact sites, and variant distribution.</li> <li> <b>July 7, 2020</b>: Annotation tracks released: <a target="_blank" href="https://genome.ucsc.edu/goldenPath/newsarch.html#070720"> PhyloCSF (Codon Substitution Frequency), Microdeletions, and Human CoV</a> (multiple alignment of SARS-CoV-2, SARS-CoV-1, MERS, and three other human-infecting coronaviruses)