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 Sep 11, 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 1,821,074
sequences:
sequence names and ID numbers used for full-length analyses,
or on a Spike alignment containing 2,465,964
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
Aug 22, 2021
Table of the most common natural forms of spike representing variants of interest
- Our cov.lanl.gov listing of commonly found Spike forms of variants of interest and variants of variants that are currently circulating or have transiently emerged in 2021 can be found here.
- A description of the contents and useful addendums can be found here.
Jul 21, 2021
Variant Visualizer is a new tool that provides multiple options and output styles for visualizing CoV-2 variants. Variant Visualizer graphical output is provided as a png or pdf, and the appearance of the output can be refined interactively.
| Name | Description |
|---|---|
| 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. |
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
