94b6137388725543913544bca8147518a9c3444f kate Thu Sep 24 15:57:30 2020 -0700 Ana and Max contributions merged in. refs #25217 diff --git src/hg/htdocs/covid19.html src/hg/htdocs/covid19.html index 5239d54..56df441 100755 --- src/hg/htdocs/covid19.html +++ src/hg/htdocs/covid19.html @@ -1,253 +1,255 @@ <!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> <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 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 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. +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 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 +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>. +<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" 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> <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> <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 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) </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" > 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> </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> <li> NIH Office of Data Science Strategy <a target="_blank" href="https://datascience.nih.gov/covid-19-open-access-resources">Open-Access Data and Computational Resources to Address COVID-19</a> </li> <li> European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL-EBI) and partners: <a target="_blank" href="https://www.covid19dataportal.org/"> COVID-19 Data Portal</a> </li> <li> China National Center for Bioinformation: <a target="_blank" href="https://bigd.big.ac.cn/ncov?lang=en"> 2019 Novel Coronavirus Resource</a> </li> <li> CDC <a target="_blank" href="https://github.com/CDCgov/SARS-CoV-2_Sequencing"> SARS-CoV-2 Sequencing Resources</a> on GitHub </li> <li> Nextstrain open-source tracking of pathogen evolution: <a target="_blank" href="https://nextstrain.org/ncov">SARS-Cov2 browser</a> (strain tree, geographical mapping)</li> <li> NCBI sequence database search, publication list, and genome display: <a href="https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/" target="_blank"</a>NCBI SARS-CoV-2 Sequences</a></li> <li>Virus Pathogen Resource: <a target="_blank" href="https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov">VIPR SARS-CoV-2 resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies)</li> <li>CDC: <a target="_blank" href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html">Cases in U.S.</a>, updated daily. </li> <li>CDC data as <a href = "https://bit.ly/coronaPerCapita" target = _blank><em>per capita</em> map</a> of the states. </li> <li>Johns Hopkins University: <a target="_blank" href="https://coronavirus.jhu.edu/map.html"> Coronavirus Resource Center</a></li> <li> CitizenScience.org: <a target="_blank" href="https://www.citizenscience.org/covid-19/" > COVID-19 citizen science and crowdsourcing projects</a> </li> <li>Wikipedia: <a target="_blank" href="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2">Severe acute respiratory syndrome coronavirus 2</a></li> <li> Nature News graphical guide to vaccine designs: <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"> 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> <!--#include virtual="$ROOT/inc/gbPageEnd.html"-->