599d664ddcf01de9da445c09ada1f199ade1f5ed kate Tue Feb 23 13:07:19 2021 -0800 Update intro paragraph and add news item to COVID landing page, to highlight variant and mutations tracks. diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index 500906c..8826c63 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,59 +1,71 @@ <!DOCTYPE html> <!--#set var="TITLE" value="COVID-19 Research at UCSC" --> <!--#set var="ROOT" value="." --> <!--#include virtual="$ROOT/inc/gbPageStart.html"--> <h1>COVID-19 Research at UCSC <span> <font size=-1 style="padding-left: 10px; padding-right: 10px; margin-left: 15px;"> -<a href="#news">Updated: February 03, 2021</a></font></span></h1> +<a href="#news">Updated: February 23, 2021</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). The disease spread rapidly worldwide 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 thousands of viral samples has helped researchers study mechanisms of infection, transmission and response of the human immune system. -Since the beginning of SARS-CoV-2 circulation in humans, the viral genome has been accummulating -mutations. Compared to other RNA viruses its mutation rate is low, but enough variants are known -to determine how samples cluster into groups and how they are related (see COVID-19 transmission map). -</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 treatments and a vaccine for this devastating illness by fast-tracking visualization of genome sequences and analyses in the <a target="_blank" href="/cgi-bin/hgGateway?db=wuhCor1">UCSC Genome Browser for SARS-Cov-2</a>. Moreover, we are incorporating relevant biomedical datasets such as single-cell lung gene expression into the <a target="_blank" href="/singlecell.html">UCSC Cell Browser</a>, and are creating data tracks of <a target="_blank" href="#covidHgiGwas">COVID-19 annotations in our Human Genome Browsers</a> as datasets become publicly available. These annotations can further understanding of the human genetic determinants of infection susceptibility, disease severity, and outcomes. </p> <p> +Since the beginning of SARS-CoV-2 circulation in humans, the viral genome has been accummulating +mutations. Compared to other RNA viruses its mutation rate is low, but enough variants are known +to determine how samples cluster into groups and how they are related (see COVID-19 transmission map). +Mutations identified as important medically and epidemiologically are displayed in SARS-Cov-2 browser +tracks +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts">Variants of Concern</a> and +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&g=spikeMuts">Spike Mutations</a>. +Investigations of antibody resistance of viral mutations are available in the +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&g=abEscape">Antibody Escape</a> track collection. +The B.1.1.7 variant of the virus, first identified in the UK and characterized as more infectious, +was first confirmed in the US in late December 2020. +The +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&g=lineageB_1_1_7_US">B.1.1.7 in USA</a> track +provides a phylogenetic view of the first sequences from the US, and links to view phylogenetic analysis of +the subsequently identified geographic clusters (in New York, California, Colorado and Florida). +</p> +<p> 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" @@ -144,30 +156,34 @@ 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>February 17, 2021</b>: +Release of SARS-Cov-2 + <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts" target="_blank"> Variants of Concern</a> +track, displaying amino acid and nucelotide mutations in three "Variants of Concern" (B.1.1.7, B.1.351, and P.1) and one "Variant of Interest" (B.1.429, first identified in California), as defined in late January 2021. <li><b>January 29, 2021</b>: <a target="_blank" href="goldenPath/newsarch.html#012921"> January 29th SARS-CoV-2 update</a> - This update includes new data on sequence variants and phylogeny, spike protein amino-acid mutations, and antibody escape.</li> <li><b>January 8, 2021</b>: <a target="_blank" href="goldenPath/newsarch.html#010821"> January 8th SARS-CoV-2 update</a> - This update includes an updated track as well as three new tracks for the <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank">coronavirus genome browser</a>, and a track for the <a href="/cgi-bin/hgTracks?db=hg19" target="_blank">hg19/GRCh37</a> and <a href="/cgi-bin/hgTracks?db=hg38" target="_blank">hg38/GRCh38</a> human assemblies. </li> <li>