COVID-19 Viral Genome Analysis Pipeline COVID-19 Viral Genome Analysis Pipeline home COVID-19 Viral Genome Analysis Pipeline home
COVID-19 Viral Genome Analysis Pipeline
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This website provides analyses and tools for exploring accruing mutations in hCoV-19 (SARS-CoV-2) geographically and over time, with an emphasis on the Spike protein, using data from GISAID.

The SARS-CoV-2 sequence data used for these analyses was updated from GISAID on Dec 3, 2021.

With the ever growing database of sequences in GISAID, sometimes the web connection times out before the analysis is complete. If you have this problem, please check "email results" and an email with a link will be sent to you when the job is complete.


Nov 30, 2021
An updated list of Spike variant mutations at the protein level is now available. These are offered as suggestions for reference reagents for experimental testing of commonly circulating Spike variants. The most common forms of Spike for the Omicron variant lineage (B.1.1.529), as well as for the B.1.640 lineage, are now included. See “Spike variants” on blue bar at the top of the pages.
The alignments (fasta files) of natural sequences corresponding to our suggestions for variant reference sequences are now available through the GISAID initiative, for both Spike and for full length coding regions: -> EpiCoV -> Downloads -> LANL alignments.

Nov 29, 2021
Please note: Our automated alignments are currently problematic for Omicron, B.1.1.529, in the regions neighboring the Spike NTD insertions and deletions. We hope resolve this issue by our next update of GISAID data, and apologize for any inconvenience.

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Embers plot, See data

Data Summaries

These analyses are updated several times a week. Our web-based tools can focus on specific geographic regions and time frames, using the links listed under “Tools” in the blue menu bar.

Current data shared through GISAID

How to cite


We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID on which this research is based. The original data are available from

This COVID-19 response analysis pipeline is supported by: 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.

GISAID data provided on this website is subject to GISAID’s Terms and Conditions

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