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 May 22, 2022.

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.


Jan 9, 2022
Our updated variant reference sequence fasta files for Spike and the full length genome are available through the GISAID downloads, in the LANL folder. These fasta files include reference sequences representative of the most common form of several Omicron variants. The updated spreadsheet describing the sequences and mutations, as well as notes regarding the Omicron updated sequences are available both here in “Curated Variants" and through the LANL page at GISAID.

Dec 5, 2021
Variant forms of Spike among B.1.1.529 complete genome alignments can be found summarized in our Most common spike forms based on Pango lineage designations listings.
Updated notes on Omicron variant dynamics based on GISAID sequences are now available at under the Spike Variants: Notes on Specific Variants. Reference sequence alignments are provided at After logging in, they can be found under “Downloads” and “LANL alignment”.

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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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