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. 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).
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 UCSC Genome Browser for SARS-Cov-2. Moreover, we are incorporating relevant biomedical datasets such as single-cell lung gene expression into the UCSC Cell Browser, and are creating data tracks of COVID-19 annotations in our Human Genome Browsers as datasets become publicly available. These annotations can further understanding of the human genetic determinants of infection susceptibility, disease severity, and outcomes.
A manuscript describing The UCSC SARS-CoV-2 Genome Browser, was published in the September 9 issue of Nature Genetics.
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