This application compares primer sequences with known SARS-CoV-2 variants from the NCBI GenBank 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:
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2013) GenBank. Nucleic acids research, 41(Database issue), D36-42. DOI: 10.1093/nar/gks1195 PMCID: 3531190
Gangavarapu, K., Latif, A.A., Mullen, J.L., Alkuzweny, M., Hufbauer, E., Tsueng, G., Haag, E., Zeller, M., Aceves, C.M., Zaiets, K., Cano, M., Zhou, X., Qian, Z., Sattler, R., Matteson, N.L., Levy, J.I., Lee, R.T.C., Freitas, L., Maurer-Stroh, S., … Hughes, L.D. (2023) Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources. Nature Methods, 20(4), 536–540. DOI: 10.1038/s41592-023-01770-w
Tsueng, G., Mullen, J.L., Alkuzweny, M., Cano, M., Rush, B., Haag, E., Lin, J., Welzel, D.J., Zhou, X., Qian, Z., Latif, A.A., Hufbauer, E., Zeller, M., Andersen, K.G., Wu, C., Su, A.I., Gangavarapu, K., Hughes, L.D. (2023) Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nature Methods, 20(4), 512–522. DOI: 10.1038/s41592-023-01769-3
Robinson, J. T., Thorvaldsdottir, H., Turner, D., & Mesirov, J. P. (2023). igv.js: An embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics, 39(1), btac830. DOI: 10.1093/bioinformatics/btac830.