06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index 56df441..bde690a 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,166 +1,226 @@ <!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 23, 2020</a></font></span></h1> +<a href="#news">Updated: November 13, 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). 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>. +<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 +<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> 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" + 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> </font> </div> </div> </div> <style> img { width: 100%; margin: 15px 0 !important; } </style> <div class="row"> <!-- Genome browser --> <div class="col-md-6"> <h2>UCSC Genome Browser view of SARS-CoV-2 genomic datasets</h2> - <a href="../cgi-bin/hgTracks?db=wuhCor1" target="_blank"> - <img src="../images/sarsCov2SpikeProteinsSession.png"></a> + <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank"> + <img src="/images/sarsCov2SpikeProteinsSession.png"></a> <br> Video tutorial: Using the <a href = http://bit.ly/ucscVid20 target = _blank>coronavirus browser</a>. </div> <!-- Cell browser --> <div class="col-md-6"> <h2>COVID-19 and Lung gene expression data in the UCSC Cell Browser:</h2> <p>COVID-19 Datasets: <ul> <li><a href="https://covid19-balf.cells.ucsc.edu" target="_blank">Bronchoalveolar Immune Cells in COVID-19</a> <li><a href="https://covid-airways.cells.ucsc.edu" 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 "genomic contact tracing". + 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 "real time". + 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="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas" target="_blank"> +<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 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 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"> +<a target="_blank" href="/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"> +href="/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) </li> <li><b>May 29, 2020</b>: Public track hub <a target="_blank" href="http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/COVID19_Hub.html"> GENCODE annotation of COVID-19 associated genes</a> released. View in <a target="_blank" -href="../cgi-bin/hgTracks?hubUrl=http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/hub.txt&genome=hg38&position=lastDbPos" > +href="/cgi-bin/hgTracks?hubUrl=http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/hub.txt&genome=hg38&position=lastDbPos" > browser</a>. </li> <li><a target="_blank" href="goldenPath/newsarch.html#051220">Video: Coronavirus Browser SARS CoV-2</a></li> <li><a target="_blank" href="goldenPath/newsarch.html#050420">May data release for SARS-CoV-2 genome browser</a></li> <li><a target="_blank" href="goldenPath/newsarch.html#040320">April data release for SARS-CoV-2 genome browser</a></li> +<li><b>February 7, 2020: </b><a target="_blank" +href="https://www.soe.ucsc.edu/news/coronavirus-genome-posted-ucsc-genome-browser"> +Released initial SARS-CoV-2 genome browser</a></li> </ul> <h2 id="related">Related publications and data resources</h2> <ul> <li> Preprints of research manuscripts: <a href="https://connect.biorxiv.org/relate/content/181" target="_blank">BioRxiv/MedRxiv COVID-19 Collection</a> (all freely available)</li> <li><a target="_blank" href="https://pages.semanticscholar.org/coronavirus-research">COVID-19 Open Research Dataset</a> of scholarly literature</li> <li> GISAID <a target="_blank" href="https://gisaid.org">the main repository of SARS-CoV-2 sequences</a> </li> @@ -219,31 +279,31 @@ <a target="_blank" href="https://www.nature.com/articles/d41586-020-01221-y"> The Race for Coronavirus Vaccines</a> </li> <li> <a target="_blank" href="https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html"> Inside the Coronavirus Genome</a>, and <a target="_blank" href="https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html"> How Coronavirus Mutates and Spreads</a>, The New York Times </li> </ul> <h2 id="funding">Funding</h2> <p> -The <a target="_blank" href="https://genome.ucsc.edu"> +The <a target="_blank" href=".."> UCSC Genome Browser</a> is a publicly available web resource serving the research community since July 2000. Both the Genome Browser and UCSC Cell Browser are funded by the <a target="_blank" href="https://www.genome.gov/">NIH National Human Genome Research Institute</a>. In addition to this funding, the COVID-19 projects here are funded by generous supporters including: several anonymous donors; Pat and Roland Rebele; Eric and Wendy Schmidt by recommendation of the <a target="_blank" href="https://schmidtfutures.com/">Schmidt Futures</a> program; the Center for Information Technology Research in the Interest of Society (<a target="_blank" href="https://citris-uc.org/">CITRIS</a>); and the University of California Office of the President (<a target="_blank" href="https://www.universityofcalifornia.edu/uc-system/office-of-the-president">UCOP</a>). To contribute, click <a target="_blank" href="https://secure.ucsc.edu/s/1069/bp18/interior.aspx?sid=1069&gid=1001&pgid=780&cid=1749&dids=645"> here</a>. </p>