In early 2020, this website was created to provide analysis tools for exploring accruing mutations in SARS-CoV-2 geographically and dynamically over time, with an emphasis on the evolution of the Spike protein. It used sequences and metadata provided by GISAID (Khare et al. China CDC Weekly, 2021 3(49): 1049-1051), providing sequence analysis as data was released. The analysis provided here was a primary source of data analysis regarding newly emergent variants for the SAVE project (DeGrace et al. Nature. 2022 May;605(7911):640-652), and this public interactive web interface was provided as a public resource to scientists in the global community.

Our project has ended, and we stopped updating this web site on September 9, 2026. At this point we included 17,596,910 SARS-CoV-2 sequences and their linked metadata from GISAID, and the data set is summarized here:

We are leaving some of the analysis tools up to facilitate retrospective exploration of this data and the evolution of this virus by mutations, Pango lineage designations (https://cov-lineages.org/), dates, and geographic regions. Current data can be obtained through GISAID.

Frequencies of Key Pango Lineage Groupings Over Time


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Acknowledgements

We gratefully acknowledge the authors of the data from originating and submitting laboratories of the sequences from GISAID on which this research is based, and the team at GISAID who made our work possible. The original data and more recent updates are available from https://www.gisaid.org.

The GISAID data analysis provided on this website is subject to GISAID’s Terms of Use, and the analysis tools presented on this web site were included with GISAID review and approval.

We thank the dedicated work of Angie Hinrichs, who regularly provided us with full UShER updates of Pango lineage designations (McBroome et al. Mol Biol Evol. 2021 Dec 9;38(12):5819-5824).

Cornelius Roemer provided public summaries that we relied on to stay up-to-date with Pango lineage designation descriptions (Rambaut et al. 2020 Nature Microbiology 5:1403-1407).

This COVID-19 response analysis pipeline was supported by a series of grants over its 6 years of funding. The key grants included: The Laboratory Directed Research and Development program of Los Alamos National Laboratory (20200706ER), and by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Interagency Agreement No. AAI12007-001-00000, CEIRR project National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93021C00015.