38c888f9318cb5a7efba271865f11f1b8320573e lrnassar Fri Jan 8 09:47:41 2021 -0800 Fifth coronavirus news announcement refs #26777 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 975ea3e..94c3582 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -37,30 +37,125 @@ <li><a href="#2006">2006 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> +<!-- ============= 2021 archived news ============= --> +<a name="2021"></a> + +<a name="010821"></a> +<h2>Jan. 8, 2020 January 8th SARS-CoV-2 update</h2> +<p> +We are pleased to start the year with our fifth data release for the <a href="/cgi-bin/hgTracks?db=wuhCor1" +target="_blank">coronavirus genome browser</a>. (See also our <a +href="#040320">first</a>, <a href="#050420">second</a>, <a href="#080720">third</a>, +and <a href="#102120">fourth</a> releases)</p> + +<p> +This update includes an updated track as well as three new tracks for +the <a href="/cgi-bin/hgTracks?db=wuhCor1" +target="_blank">coronavirus genome browser</a>, and a track for the <a +href="/cgi-bin/hgTracks?db=hg19" target="_blank">hg19/GRCh37</a> and <a +href="/cgi-bin/hgTracks?db=hg38" target="_blank">hg38/GRCh38</a> human assemblies. Worth note is +the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US" +target="_blank">B.1.1.7 in USA</a> +track which shows substitution and deletion variants in the <b>B.1.1.7 lineage</b>, known for its +rapid spread in England in November and December 2020, alongside the first nine genome +sequences in the United States that were assigned to the lineage.</p> + +<p> +We have also updated our <a target="_blank" href="/cgi-bin/hgPhyloPlace">web interface</a> +to <a target="_blank" href="https://github.com/yatisht/usher">UShER</a>, a tool for +placing new SARS-CoV-2 sequences in a global phylogenetic tree, +to include <a target="_blank" href="https://www.cogconsortium.uk/data/">COG-UK</a> +sequences available as of Dec. 30, 2020 including thousands of new sequences in +the B.1.1.7 lineage.</p> + +<p> +Clicking on any of the track titles below will lead to the track description page, +which includes additional information and allows for configuration of various display options.</p> +<p> +This release includes the following tracks:<br><br></p> + +<ul><li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US"> +B.1.1.7 in USA</a> - This track shows single-nucleotide variants +and deletions from the SARS-CoV-2 reference genome in the B.1.1.7 consensus sequence +and the first nine genome sequences in the United States that were assigned to B.1.1.7. +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=escape"> +Antibody escape</a> - This track contains mutations +in the Spike protein that attenuate monoclonal and serum antibody neutralization.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=pbmShanghai"> +S Antib Pept Array</a> - This track shows intensities of a microarray spotted +with short peptides derived from the S protein. Sera from both convalescent COVID-19 +and control patients were screened on the peptide microarray for both IgG and IgM responses.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=covidHgiGwasR4Pval"> +COVID GWAS v4 (hg38)</a> - This track set shows the results of the <a target="_blank" +href="https://www.covid19hg.org/blog/2020-11-24-covid-19-hgi-results-for-data-freeze-4-october-2020/"> +GWAS Data Release 4 (October 2020)</a> from the <a target="_blank" href="https://www.covid19hg.org/"> +COVID-19 Host Genetics Initiative (HGI)</a> which aims to identify the genetic determinants of +SARS-CoV-2 infection susceptibility, disease severity and outcomes.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=sarsCov2PhyloPub"> +Updated - Phylogenetic Tree and Variants from High-coverage Sequences in Public Databases</a> +- Updated from release <b>28-08-20</b> to <b>28-10-20</b>. This track displays a phylogenetic tree +inferred from SARS-CoV-2 genome sequences from <a +href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049" +target="_blank">GenBank</a>, <a href="https://www.cogconsortium.uk/data/" +target="_blank">COG-UK</a> and the <a href="https://bigd.big.ac.cn/ncov/release_genome" +target="_blank">China National Center for Bioinformation</a>, and variants found +in the sequences. Since this track is sourced from public databases, we can offer VCF files with +sequence variants for <a href="https://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" +target="_blank">download</a>.</li> +</ul> + +<p><br> +We would like to thank the publication authors <a target="_blank" +href="https://www.ncbi.nlm.nih.gov/pubmed/32895485">Li <em>et al</em></a> and +<a target="_blank" +href="https://www.biorxiv.org/content/10.1101/2020.11.06.372037v1">Liu <em>et al</em></a> for +making these data available. We would also like to thank +<a href="http://public.gi.ucsc.edu/~jferna10/" target="_blank">Jason Fernandes</a>, +<a href="https://www.cogconsortium.uk/" target="_blank">COG-UK</a>, +<a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">GenBank</a>, +the <a href="https://gisaid.org/" target="_blank">GISAID Initiative</a>, +the <a href="https://www.covid19hg.org/" target="_blank">COVID-19 Host Genetics Initiative (HGI)</a> +and their <a target="_blank" href="https://www.covid19hg.org/partners/">partners</a>, as well as +Rachel Liao, Juha Karjalainen, and Kumar Veerapen from the <a target="_blank" +href="https://www.broadinstitute.org/">Broad Institute</a>.</p> + +<p> +These tracks are made possible due to the worldwide efforts of scientists, including the +<a href="/staff.html" target="_blank">Genome Browser team</a>. We will continue to +provide SARS-COVID-2 resources as they become available. For the latest data, see our +<a href="http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" +target="_blank">preview site</a>. Note that content on our preview server has not +undergone our QA process, and is subject to change at any time.</p> + <!-- ============= 2020 archived news ============= --> <a name="2020"></a> <a name="122320"></a> <h2>Dec. 23, 2020 New ClinVar Interpretations track for human (hg19/hg38)</h2> <p> We are pleased to release a new track, <b>ClinVar Interpretations</b>, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">ClinVar Composite</a>. It is the first track to use our bead graph display, which is a variation of our existing <a target="_blank" href="#062019">lollipop display</a>.</p> <p> The <b>ClinVar Interpretations track</b> displays the genomic positions of individual variant submissions and interpretations of the clinical significance, as well as their relationship to disease in the ClinVar database. As seen on the image below, the variants are classified into @@ -676,31 +771,31 @@ target="_blank">Sun <em>et al</em></a>, and <a href="https://www.biorxiv.org/content/10.1101/2020.06.08.141127v1" target="_blank">Turakhia <em>et al</em></a> for making these data available. We would also like to thank <a href="http://www.robertlanfear.com/" target="_blank"> Rob Lanfear</a>, <a href="https://www.biorxiv.org/content/10.1101/2020.06.02.130955v1" target="_blank">Irwin Jungreis</a>, <a href="http://zhanglab.net/" target="_blank"> Qiangfeng Cliff Zhang</a>, <a href="http://public.gi.ucsc.edu/~jferna10/" target="_blank"> Jason Fernandes</a>, <a href="https://snerli.wordpress.com/about/" target="_blank"> Santrupti Nerli</a>, <a href="https://www.lji.org/faculty-research/labs/peters/#overview" target="_blank">Bjoern Peters</a>, the <a href="https://research.fhcrc.org/bloom/en.html" target="_blank">Bloom Lab</a>, the <a href="https://www.weizmann.ac.il/pages/" target="_blank">Weizmann Institute of Science</a> and the <a href="https://gisaid.org/" target="_blank">GISAID Initiative</a>.</p> <p> These tracks are made possible due to the worldwide efforts of scientists, including the -<a href="/staff.html" target="_blank">Genome Browser team</a>. Will will continue to +<a href="/staff.html" target="_blank">Genome Browser team</a>. We will continue to provide SARS-COVID-2 resources as they become available. For the latest data, see our <a href="http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" target="_blank">development site</a>. Note that content on our preview server has not undergone our QA process, and is subject to change at any time.</p> <a name="101520"></a> <h2>Oct. 15, 2020 Updated Ensembl gene tracks for 47 assemblies (v101)</h2> <p> We are pleased to announce an update to the <a href="http://uswest.ensembl.org/info/genome/genebuild/index.html" target="_blank"> Ensembl gene annotation</a> tracks to <strong>v101</strong> for the following assemblies:</p><br> <div class="container"> <div class="row"> <div class="col-sm-4">