4b5c55170859286c0204cffcf647ac2d1ae886a2 max Sat Mar 21 08:04:24 2020 -0700 covid19 index page diff --git src/hg/htdocs/covid19/index.html src/hg/htdocs/covid19/index.html index 122226d..266f97b 100755 --- src/hg/htdocs/covid19/index.html +++ src/hg/htdocs/covid19/index.html @@ -1,292 +1,168 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <title>UCSC Ebola Portal</title> <link rel="stylesheet" href="../style/HGStyle.css" type="text/css"> <link rel="stylesheet" href="../style/encodeProject.css" type="text/css"> - <link rel="stylesheet" href="ebolaPortal.css" type="text/css"> + <link rel="stylesheet" href="covid.css" type="text/css"> </head> <body style="margin:0;"> <!--#include virtual="../inc/ebola.topbar.html"--> <div class="header"> <span class="txt"> UCSC Covid19 Portal</span> <span class="subHeader">Resources for the pandemic</span> </div> <div style="margin:8px; margin-right:16px;"> <table> <tr> <td colspan="3"> <div style="margin-top: 0; margin-left: 10px;" class="wrapper"> <div class="bar"><h4 class="title">About</h4></div> <div class="content"> <p> We have fast-tracked the <a target="_blank" href="../cgi-bin/hgTracks?db=wuhCor1">UCSC SARS-Cov2 Genome Browser</a> - This site also provides related tools and + <!--This site also provides related tools and information that can be used to further the understanding of SARS-Cov2 and its disease Covid19. + --> </p> <p> Downloads for the SARS-Cov2 genome in the UCSC Genome Browser can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#sarscov2" target="_blank">here</a>. </p> </div><!--end content--> </td> </tr> <!-- screenshot launchers 2x2 matrix --> <tr> <!-- Browser image linking to browser CGI --> <td> <div style="margin-top:0; margin-left:10px; margin-right:10px" class="wrapper"> <div class="bar"><h4 class="title">Explore the SARS-Cov2 Genome with the UCSC Browser</h4></div> <div class="content"> <a href="../cgi-bin/hgTracks?db=wuhCor1" target="_blank"><img class="screenshot" src="../images/ebolaBrowser.png"></a> </div> </div> </td> <!-- Incidence graph linked to CDC site --> <td> <div style="margin-top:0; margin-right: 10px;" class="wrapper"> - <div class="bar"><h4 class="title">Learn about the 2014 outbreak</h4></div> - <a href="http://www.cdc.gov/vhf/ebola/" target="_blank"><img class="screenshot" src="../images/Graph_Diseased_Ebola_2014.png"></a> + <div class="bar"><h4 class="title">Explore lung single cell datasets</h4></div> + <a href="https://cells.ucsc.edu/?ds=teichmann-asthma" target="_blank"><img class="screenshot" src="../images/Graph_Diseased_Ebola_2014.png"></a> </div> </td> <!-- Viral structure cartoon and launcher from ViralZone --> <td> <div style="margin-top:0;" class="wrapper"> - <div class="bar"><h4 class="title">Read about Ebola</h4></div> - <a href="http://viralzone.expasy.org/all_by_species/207.html" target="_blank"><img class="screenshot" src="../images/Filovirus_virion_small.png"></a> + <div class="bar"><h4 class="title">What should we link here?</h4></div> + <a href="no idea" target="_blank"><img class="screenshot" src="../images/Filovirus_virion_small.png"></a> </div> </td> </tr> <!-- Publications block --> <tr> <td colspan="3"> <div style="margin-top: 15px; margin-left: 10px;" class="wrapper"> <div class="bar"><h4 class="title">Related Publications and Data Resources</h4></div> <div class="content"> <p> + Nextstrain: + <a target="_blank" href="https://nextstrain.org/ncov">SARS-Cov2 browser</a> (strain tree, geographical mapping) + <p> + <p> NCBI sequence database search, publication list, and genome display: - <a href="https://www.ncbi.nlm.nih.gov/genome/viruses/variation/ebola/" target="_blank"</a>NCBI Virus Variation Ebolavirus Resource</a> + <a href="https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/" target="_blank"</a>NCBI Covid19 page</a> </p> </p> Virus Pathogen Resource: - <a target="_blank" href="http://www.viprbrc.org/brc/home.spg?decorator=filo_ebola">VIPR Ebolavirus resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies) - <p> - Swiss Bioinformatics Institute ViralZone: - <a target="_blank" href="http://viralzone.expasy.org/all_by_species/207.html">ViralZone Ebolavirus molecular biology</a> (molecular and epidemiological information with links to SwissProt/UniProt proteins) - <p> - PLOS Ebola Flipboard: - <a href="https://flipboard.com/section/plos-ebola-collection-bRVgYj" - target="_blank">PLOS Ebola Collection</a> (all currently published articles, freely - available) + <a target="_blank" href="https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov">VIPR Covid19 resource</a> (tools for sequence and structure analysis, comparative genomics and phenotype studies) + Biorxiv preprints: + <a href="https://connect.biorxiv.org/relate/content/181" + target="_blank">Biorxiv Collection</a> (all preprints, freely available) </p> - <p> - Science Magazine collection: - <a href="http://www.sciencemag.org/site/extra/ebola/" target="_blank">Science - Magazine Special Collection: Ebola Virus</a> (freely available research and news - articles) - </p> - <p> + <!--<p> The New England Journal of Medicine resource: <a href="http://www.nejm.org/page/ebola-outbreak" target="_blank">NEJM Ebola Outbreak</a> (A collection of articles and other resources on the Ebola outbreak, including clinical reports, management guidelines, and commentary.) - </p> + </p> --> </div> </div><!--end content--> </div><!--end wrapper--> </td> </tr> <!-- Ebola Biology block --> <tr> <td colspan="3"> <div style="margin-top: 0; margin-left: 10px;" class="wrapper"> - <div class="bar"><h4 class="title">Ebola Biology</h4></div> + <div class="bar"><h4 class="title">What to put here?</h4></div> <div class="content"> <p> - Ebola virus is the causative agent of Ebola hemorrhagic fever (EHF), - a disease affecting humans and other primates. The incubation period - for EHF is 2-21 days and typical early symptoms include fever, chills, - malaise, and myalgia, followed by the onset of symptoms indicative of - multi-organ stress and subsequent failure. The disease is also characterized - by high death rates (as high as 90%) and worse yet, is highly contagious, - spreading through direct contact with infected body fluids or skin/mucus membrane - contact. - This perfect storm of conditions make the possibility of a large-scale epidemic - a very real concern. - </p> - <p> - Ebola virus and the related Marburg virus are members of the family - Filoviridae, so named for their filamentous shape. Like other Filoviruses, - Ebola is an enveloped, non-segmented, negative-stranded RNA virus. Ebola virus - particles have at their core a viral nucleocapsid composed of a helical single - stranded RNA genome wrapped around viral proteins NP, VP35, VP30, and L. The - nucleocapsid is surrounded by an outer viral envelope studded with viral - glycoprotein (GP) spikes, and viral proteins VP40 and VP24 sit between the - nucleocapsid and the envelope. - </p> - <p> - The viral life cycle begins with host cell entry through a poorly understood - mechanism. Once inside - the viral RNA-dependent RNA polymerase (L) binds the 19 kb genome as a complex with - other factors and transcribes the negative strand genome into a positive strand - mRNA to be translated by the host cell's machinery. The seven genes are ordered in - the genome as follows: 3-leader-NP-VP35-VP40-GP/sGP-VP30-VP24-L-trailer-5'. Once the - concentration of nucleocapsid protein (NP) reaches a sufficient level, the RNA - polymerase switches - modes to genome replication, producing full-length positive strand genomes to be - transcribed into negative orientation. These genomes self assemble with - other virus proteins and bud from the host cell, sheathed in host - cell membrane, thus completing the cycle. </p> </div><!--end content--> </div><!--end wrapper--> </td> </tr> <!--Antibodies panel --> <a name="antibodies"> <tr> <td colspan="3"> <div style="margin-top: 0; margin-left: 10px;" class="wrapper"> - <div class="bar"><h4 class="title">Antibody Resources</h4></div> + <div class="bar"><h4 class="title">Antibody Resources - probably no need for that?</h4></div> <div class="content"> - <p> - UC Santa Cruz is collecting - <a target=_blank href="http://hgdownload.soe.ucsc.edu/goldenPath/eboVir3/ebolaAbSequences.fasta"> - Ebola antibody sequence</a> - data and facilitating survivor blood sample exchange between researchers. - If you have sequence or blood samples that you would be willing to share - with other researchers please contact: - <A HREF="mailto:kent@soe.ucsc.edu">kent@soe.ucsc.edu</A></p> - <p> - Below we list papers and other resources related to antibody use in the treatment and vaccine development for Ebola Virus Disease. - Additional references and detail can be found in our - <a target="_blank" href="https://docs.google.com/spreadsheets/d/1xlSp_-VIh9npq_wlsHU6WYjNCDEawM8rBtLpZVlXelQ/pubhtml?gid=0&single=true&widget=true&headers=false">Antibody Resources Working Spreadsheet</a>.</p> - <ul> - <li> - Neutralizing antibodies for Kikwit strain (1999): - <a href="https://www.ncbi.nlm.nih.gov/pubmed/10364354" - target="_blank"> Ebola virus can be effectively neutralized by antibody produced in - natural human infection</a> - [<a href="http://jvi.asm.org/content/73/7/6024.full.pdf" target="_blank">PDF</a>] - <li> - Humanized mAbs (ZMapp) expressed in tobacconists (2014): - <a href="https://www.ncbi.nlm.nih.gov/pubmed/25171469" - target="_blank">Reversion of advanced Ebola virus disease in nonhuman primates with - ZMapp</a> - [<a href="http://www.nature.com/nature/journal/vnfv/ncurrent/pdf/nature13777.pdf" - target="_blank">PDF</a>] - <li> - mAbs (MB-003) cocktail (2012): - <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497800" target="_blank">Delayed treatment of Ebola virus infection with plant-derived monoclonal antibodies provides protection in rhesus macaques</a> - <li> - EBOV IgG+ sera from asymptomatic individuals and symptomatic Gabonese survivors - (2014): - <a href="https://www.ncbi.nlm.nih.gov/pubmed/24914933" - target="_blank">Identification of continuous human B-cell epitopes in the VP35, - VP40, nucleoprotein and glycoprotein of Ebola virus</a> - [<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051576/pdf/pone.0096360.pdf" - target="_blank">PDF</a>] - <li> - Mouse mAb binding sites mapped to seven antigenic regions, two highly conserved, - across all known Ebolavirus species (2013): - <a href="https://www.ncbi.nlm.nih.gov/pubmed/23702199" - target="_blank">Mapping of conserved and species-specific antibody epitopes on the - Ebola virus nucleoprotein</a> - [<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787873/pdf/nihms516287.pdf" - target="_blank">PDF</a>] - </ul> - <p> - Literature links from - <a href="http://help.iedb.org/entries/51011785-Ebola-virus-related-immune-epitope-data-curated-in-the-IEDB" - target="_blank">Reported functional EBOV-related B cell epitopes</a> (Table 2) on - the <a href="http://www.iedb.org/" - target="_blank">Immune Epitope Database and Analysis Resource</a> (IEDB) website: - </p> - <ul> - <li> - (2012) <a href="http://www.mdpi.com/1999-4915/4/4/447" - target="_blank">Structural basis for differential neutralization of ebolaviruses</a> - </li> - <li> - (2011) <a href="http://linkinghub.elsevier.com/retrieve/pii/S1521-6616(11)00242-7" - target="_blank">Characterization of Zaire ebolavirus glycoprotein-specific - monoclonal antibodies</a> - </li> - <li> - (2008) <a href="https://www.ncbi.nlm.nih.gov/pubmed/18005986" - target="_blank">Complex of a protective antibody with its Ebola virus GP peptide - epitope: unusual features of a V lambda x light chain</a> - </li> - <li> - (2008) <a href="http://dx.doi.org/10.1038/nature07082" - target="_blank">Structure of the Ebola virus glycoprotein bound to an antibody from - a human survivor</a> - </li> - <li> - (2003) <a href="http://jvi.asm.org/cgi/pmidlookup?view=long&pmid=12502822" - target="_blank">Identification of protective epitopes on ebola virus glycoprotein - at the single amino acid level by using recombinant vesicular stomatitis viruses</a> - </li> - <li> - (2000) <a href="http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=10698744" - target="_blank">Epitopes involved in antibody-mediated protection from Ebola - virus</a> - </li> - </ul> - </p> - </div><!--end content--> </div><!--end wrapper--> </td> </tr> <!-- PR Links block --> <tr> <td colspan="3"> <div style="margin-top: 0; margin-left: 10px;" class="wrapper"> - <div class="bar"><h4 class="title">General Interest Links</h4></div> + <div class="bar"><h4 class="title">General Interest Links - replace this with a link to Alexis' FAQ</h4></div> <div class="content"> + <!-- <p> Wikipedia: <a target="_blank" href="http://en.wikipedia.org/wiki/Ebola_virus_disease">Ebola virus disease</a> </p> <p> <a href="http://www.youtube.com/watch?v=qTcfnTISMDk" target="_blank">NOVA: Ebola, The Plague Fighters</a> (1995) </p> <p> <a href= "https://www.youtube.com/watch?v=jTF7i6OBGQk" target="_blank">Fighting to Contain Sierra Leone's Ebola Epidemic</a> (2014) </p> <p> <a href= "https://www.youtube.com/watch?v=l0EBQKdQyyM" target="_blank">A Popular Song in Africa about Ebola (2014)</a> </p> + --> </div> </div><!--end content--> </div><!--end wrapper--> </td> </tr> </table> </body> </html>