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 declared a pandemic by the World Health Organization on March 11, 2020.
- ++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. +
We at the UC Santa Cruz Genomics Institute are responding to the urgency of supporting biomedical research aimed at -developing therapeutics and a vaccine for this devastating illness by fast-tracking the -UCSC Genome Browser for SARS-Cov-2 -and incorporating relevant biomedical datasets such as single-cell lung gene expression into the -UCSC Cell Browser. +developing therapeutics and a vaccine for this devastating illness by fast-tracking our +visualization of the SARS-CoV-2 genome sequences and analyses, the +UCSC Genome Browser for SARS-Cov-2, +by incorporating relevant biomedical datasets such as single-cell lung gene expression into the +UCSC Cell Browser, and by creating data tracks +of +COVID-19 annotations in our Human Genome Browsers.
-A manuscript describing this work, +A manuscript describing The UCSC SARS-CoV-2 Genome Browser, was published in the September 9 issue of Nature Genetics.
Latest situation report from Nextstrain.org @@ -83,33 +93,42 @@ target="_blank">COVID-19 and Influenza Immunophenotyping
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- +September 22, 2020: +First COVID-19-related annotation track on UCSC human genome browser: + +COVID-19 GWAS: GWAS meta-analyses of studies contributed by multiple partners world-wide (18 in +this release), as part of the +COVID-19 Host Genetics Initiative, +a collaborative effort to facilitate the generation, analysis and sharing of COVID-19 host genetics research. +
- September 9, 2020: -The manuscript describing this work, +The manuscript describing the The UCSC SARS-CoV-2 Genome Browser, is now published in Nature Genetics.
- August 7, 2020: Eight new annotation tracks, presenting information about duplication regions, sequencing, gene identities, plasmid constructs, protein contact sites, and variant distribution.
- July 7, 2020: Annotation tracks released: PhyloCSF (Codon Substitution Frequency), Microdeletions, and Human CoV (multiple alignment of SARS-CoV-2, SARS-CoV-1, MERS, and three other human-infecting coronaviruses)