This application compares primer sequences with known SARS-CoV-2 variants from the GISAID database to allow for simple evaluation of their potential impact on primer effectiveness.
Logged in users can subscribe to be notified when a variant overlapping a primer set reaches a threshold fraction of observed sequences in any geographic region.
This tool has been released quickly in response to concerns about the effects of emergent viral variants on primer effectiveness. It is under active development at GitHub. Contributions, problem reports, and feature requests are welcome.
Your email address (if you have registered for an account) is used only in relation to this application as you indicate. The tool intends to reliably detect variation but comes with no warranty.
Acknowledgments:
We would like to thank the GISAID Initiative and are grateful to all of the data contributors, i.e.the Authors, the Originating laboratories responsible for obtaining the specimens, and the Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which this research is based.
Elbe, S., and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 1:33-46. DOI: 10.1002/gch2.1018 PMCID: 31565258
Note: When using results from these analyses in your manuscript, ensure that you also acknowledge the Contributors of data, i.e.“We gratefully acknowledge all the Authors, the Originating laboratories responsible for obtaining the specimens, and the Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which this research is based.”
Also, cite the following reference:Shu, Y., McCauley, J. (2017) GISAID: From vision to reality. EuroSurveillance, 22(13) DOI: 10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101