SARS-CoV-2 (Belouzard, et al. Viruses. 2012 Jun; 4(6): 1011-1033)

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.

This genome browser is based on sequence obtained from the sample Wuhan-Hu-1, obtained in December 2019 in the city of Wuhan (Hubei province, China), submitted to the Shanghai Public Health Clinical Center on January 5, 2020 and to the US National Center for Biotechnology Information on January 17, 2020.

A manuscript describing this work, The UCSC SARS-CoV-2 Genome Browser, was published in the September 9, 2020 issue of Nature Genetics.

Additional information can be found in our UCSC COVID-19 Resources page. See also our web interface to UShER, a tool for placing new SARS-CoV-2 sequences in a global phylogenetic tree.

Download sequence and annotation data:

• Using HTTP
• Using FTP

• GISAID the biggest repository of SARS-CoV-2 sequences
• Genomic epidemiology of novel coronavirus from Nextstrain, open-source real-time tracking of pathogen evolution
• COVID-19 Open Research Dataset of scholarly literature
• COVID-19 SARS-CoV-2 preprint publications from bioRxiv
• NCBI GenBank: SARS-CoV-2 Sequences
• CDC: Cases in U.S., updated at noon Mondays through Fridays
• Johns Hopkins University: Coronavirus Resource Center
• Wikipedia: Severe acute respiratory syndrome coronavirus 2

UCSC Genome Browser assembly ID: wuhCor1
NCBI Sequencing/Assembly provider ID: SARS-CoV-2 ASM985889v3
Assembly date: Jan. 2020
NCBI Accession ID: GCF_009858895.2
BV-BRC: Coronaviridae
NCBI Genome ID: 86693 (SARS-CoV-2)
NCBI Assembly ID: 15851418
NCBI BioProject ID: 485481
NCBI Virus: Novel coronavirus data hub
VIPR database: SARS-CoV-2
Viral Zone: Betacoronavirus

The UCSC SARS-CoV-2 Genome Browser is funded in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93019C00076. It was funded 2020-2021 by the NIH National Human Genome Research Institute, as part of the NHGRI UCSC Genome Browser award U41HG002371.

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).