COVID-19 Research at UCSC Updated: Jan. 12, 2022

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 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. We are also incorporating relevant biomedical datasets such as single-cell lung gene expression into the UCSC Cell Browser, and creating data tracks of 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. 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 alignment of the Pfizer and Moderna mRNA vaccine sequences to the SARS-CoV-2 genome can be viewed using the Vaccines track.

See our SARS-CoV-2 introduction page for an overview of the resources offered. A manuscript describing The UCSC SARS-CoV-2 Genome Browser was also published in the September 9, 2020 issue of Nature Genetics.

COVID-19 transmission as of May 30, 2020, from Nextstrain
COVID-19 transmission as of May 30, 2020
Latest global analysis from

UShER for real-time genomic contact tracing

UShER logo In addition to the Genome Browser, we offer a web interface to Ultrafast Sample placement on Existing tRees (UShER) (Turakhia et al.), a tool for identifying the relationships among a user's newly sequenced viral genomes and all known SARS-CoV-2 virus genomes. UShER identifies relationships between viral genomes by adding them to an existing phylogenetic tree of similar sequences that visually depicts the evolutionary relationships among the genome sequences. This approach empowers "genomic contact tracing". That is, UShER tells you whether virus genomes are closely related and therefore possibly from the same source, or if they are distantly related and the infections come from distinct sources. When newly sequenced virus genomes are added to a comprehensive tree of previously sequenced genomes, contact tracers are often able to determine where in the world those genomes came from. UShER is the only available method that can do this in "real time". Our tool places genomes onto a comprehensive global phylogeny of more than 80,000 virus genomes in less than one second. More information about UShER can be found on the UCSC news article, New tools enable rapid analysis of coronavirus sequences and tracking of variants. The number of genome sequences available has increased to 5.6 million since the article was initially published with 1.2 million sequences on May 2021.

The CDC COVID-19 Genomic Epidemiology Toolkit now includes a training module for UShER! Module 3.3 includes a video, slides (PDF), and links to more resources.

Example output of UShER
Example UShER results displayed using Nextstrain. Sequences representing a hypothetical outbreak are yellow; previously sampled sequences are blue. Branches are labeled by nucleotide mutations.



The UCSC Genome Browser is a publicly available web resource serving the research community since July 2000. Both the Genome Browser and UCSC Cell Browser are funded by the NIH National Human Genome Research Institute. The Genome Browser recieved funding from the NIAID, National Institute of Allergy and Infectious Disease. In addition to this funding, the COVID-19 projects here are funded by generous supporters including: several anonymous donors; Pat and Roland Rebele; Eric and Wendy Schmidt by recommendation of the Schmidt Futures program; the Center for Information Technology Research in the Interest of Society (CITRIS); and the University of California Office of the President (UCOP). To contribute, click here.