This application compares primer sequences with known SARS-CoV-2 and RSV 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
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), Article 11. DOI: 10.1038/s41564-020-0770-5
Rsv-lineages/lineage-designation-A. (2024). [Computer software]. RSV Genotyping Consensus Consortium. https://github.com/rsv-lineages/lineage-designation-A (Original work published 2023)
Rsv-lineages/lineage-designation-B. (2024). [Computer software]. RSV Genotyping Consensus Consortium. https://github.com/rsv-lineages/lineage-designation-B (Original work published 2023)
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
Software Tools:
Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773 DOI: 10.21105/joss.03773.
Colquhoun & Jackson. Cov-lineages/scorpio. (2024). [Python]. CoV-lineages. https://github.com/cov-lineages/scorpio (Original work published 2021)
Garrison, Erik, and Gabor Marth. “Haplotype-Based Variant Detection from Short-Read Sequencing.” ArXiv:1207.3907 [q-Bio], July 20, 2012. http://arxiv.org/abs/1207.3907.
Jackson, B. (2022). gofasta: Command-line utilities for genomic epidemiology research. Bioinformatics, 38(16), 4033–4035. DOI: 10.1093/bioinformatics/btac424
Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. DOI: 10.1093/bioinformatics/bty191 .
Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., & Köster, J. (2021). Sustainable data analysis with Snakemake (10:33). F1000Research. DOI: 10.12688/f1000research.29032.2
O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution, 7(2), veab064. DOI: 10.1093/ve/veab064
Quinlan, Aaron R, and Ira M Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics (Oxford, England) 26 (2010): 841–42. DOI: 10.1093/bioinformatics/btq033
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.