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COVID-19 Viral Genome Analysis Pipeline
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NOTICE:

We are in the process of upgrading our web servers to accommodate the recent great increases in sequence data coming to us through GISAID. Until we get the new servers running, we will have some delays in our daily GISAID updates. Please note date the data was uploaded when you use our analyses tools; it may be a few days old. Sorry for any inconvenience, we hope to resolve this very soon.

Thanks for your patience,
The cov.lanl.gov staff


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 Apr 13, 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.

The analyses provided are based on a trimmed full length SARS-CoV-2 alignment containing 679,143 sequences:
sequence names and ID numbers used for full-length analyses,
or on a Spike alignment containing 880,195 sequences:
sequence names and ID numbers used for spike-only analyses.

The details of the analyses are described in:
Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI*, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, and Montefiori DC.
*on behalf of the Sheffield COVID-19 Genomics Group
Cell, June 2020
DOI:10.1016/j.cell.2020.06.043

News

Nov 16, 2020
We have added a bunch of new antibody features to the Variantion Summaries spreadsheet and updated it.

Nov 9, 2020
The slides of a talk given Nov. 5, 2020 as part of the IEDB annual workshop are available. The slides describe the data included at cov.lanl.gov, and an example of how to use the analyses tools provided at this web site.

See more

 


See data



Acknowledgements

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 https://www.gisaid.org

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

Questions or comments? Contact us at seq-info@lanl.gov

 
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