46993f5d2f87efc87bdd533ccbf05ae98d0142f3 max Sat Mar 21 07:19:46 2020 -0700 adding covid page diff --git src/hg/htdocs/covid19/index.html src/hg/htdocs/covid19/index.html new file mode 100755 index 0000000..122226d --- /dev/null +++ src/hg/htdocs/covid19/index.html @@ -0,0 +1,292 @@ +<!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"> +</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 + 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> + </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> + </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> + 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> + </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) + </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> + 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> + + </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="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="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="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>