bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/ebolaPortal/index.html src/hg/htdocs/ebolaPortal/index.html index ddd76d6344e..adba39bdc3a 100755 --- src/hg/htdocs/ebolaPortal/index.html +++ src/hg/htdocs/ebolaPortal/index.html @@ -1,295 +1,295 @@ <!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 Ebola Genome Portal</span> <span class="subHeader">Resources for the 2014 West Africa Outbreak</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> The 2014 Ebola epidemic in West Africa has stirred international response and renewed efforts to develop effective preventative and treatment options. In response to a request for help from vaccine researchers, we have fast-tracked the <a target="_blank" href="../cgi-bin/hgTracks?db=eboVir3">UCSC Ebola Genome Browser</a> built with viral sequences from previous outbreaks as well as the 2014 outbreak. This site also provides related tools and information that can be used to further the understanding of Ebola. </p> <p> Downloads for the Ebola genome in the UCSC Genome Browser can be found - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#ebola_virus" target="_blank">here</a>. + <a href="http://hgdownload.gi.ucsc.edu/downloads.html#ebola_virus" 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 Ebola Genome with the UCSC Browser</h4></div> <div class="content"> <a href="../cgi-bin/hgTracks?db=eboVir3" 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"> + <a target=_blank href="http://hgdownload.gi.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>