The SARS-CoV-2 coronavirus emerged in December 2019 as a novel human pathogen causing a severe acute respiratory syndrome (COVID-19). The disease spread rapidly worldwide and was declared a pandemic by the World Health Organization on March 11, 2020.
Genome sequencing of thousands of viral samples has helped researchers study mechanisms of infection, transmission and response of the human immune system. We at the UC Santa Cruz Genomics Institute -are responding to the urgency of supporting biomedical research aimed at -developing treatments and a vaccine for this devastating illness by fast-tracking -visualization of genome sequences and analyses in the +are responding to the urgency of biomedical research to develop treaments and vaccines for this +devastating illness by fast-tracking visualization of genome sequences and analyses in the UCSC Genome Browser for SARS-Cov-2. -Moreover, we are incorporating relevant biomedical datasets such as single-cell lung gene +We are also incorporating relevant biomedical datasets such as single-cell lung gene expression into the -UCSC Cell Browser, and are creating data tracks +UCSC Cell Browser, and creating data tracks of -COVID-19 annotations in our Human Genome Browsers -as datasets become publicly available. These annotations can further understanding of the +COVID-19 annotations in our Human Genome Browsers. +These annotations can further understanding of the human genetic determinants of infection susceptibility, disease severity, and outcomes.
Since the beginning of SARS-CoV-2 circulation in humans, the viral genome has been accummulating -mutations. Compared to other RNA viruses its mutation rate is low, but enough variants are known -to determine how samples cluster into groups and how they are related (see COVID-19 transmission map). -Mutations identified as important medically and epidemiologically are displayed in SARS-Cov-2 browser +mutations. +Mutations identified as important medically and epidemiologically are displayed in SARS-Cov-2 +browser tracks Variants of Concern and Spike Mutations. Investigations of antibody resistance of viral mutations are available in the -Antibody Escape track collection. -The B.1.1.7 variant of the virus, first identified in the UK and characterized as more infectious, -was first confirmed in the US in late December 2020. -The -B.1.1.7 in USA track -provides a phylogenetic view of the first sequences from the US, and links to view phylogenetic analysis of -the subsequently identified geographic clusters (in New York, California, Colorado and Florida). +Antibody Escape track +collection.
A manuscript describing -The UCSC SARS-CoV-2 Genome Browser, was published in the September 9 issue of Nature Genetics. +The UCSC SARS-CoV-2 Genome Browser, was published in the September 9, 2020 issue of +Nature Genetics.
- Latest situation report from Nextstrain.org + Latest global analysis from Nextstrain.org
In addition to the Genome Browser, we offer a
