This website provides analyses and tools for exploring accruing mutations in the Spike protein of SARS-CoV-2, geographically and over time, using data from the Global Initiative for Sharing All Influenza Data (GISAID) SARS-CoV-2 database.
The SARS-CoV-2 sequence data used for these analyses was updated from GISAID on Jun 28, 2020
The analyses provided are based on a trimmed full length SARS-CoV-2 alignment containing 23,960
sequence names and ID numbers used for full-length analyses,
or on a Spike alignment containing 43,047 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
In press in Cell, June 2020
May 11, 2020
| SARS-CoV-2 map
||Geographical distributions of variant sites (pie charts on a map).|
|Isotonic Regression||Isotonic Regression|
|Relative Frequency Change By Geographical Region||Relative Frequency Change By Geographical Region|
|Tracking mutations||Amino-acid variant accumulation over time (sampled frequencies as bar plots).|
| Table of mutating sites in Spike
||List of variant sites-of-interest by sequence isolate, with covarying sites.|
| Rainbow trees
||Phylogenetic distribution of variant Spike protein sites-of-interest,|
colored by country of sample origin.
| SARS-CoV-2 Sequence Locator
||Locate sequence motifs against the reference sequences;|
provide standardized numbering.
|GISAID Acknowledgements Table||Acknowledgement data for sequences used for analyses.|
Includes Accession ID, Isolate name, detailed location, Collection date, Originating lab, Submitting lab, Authors.
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