The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation
Open accessAbstract
Summary CoV-GLUE is an online web application for the interpretation and analysis of SARS-CoV-2 virus genome sequences, with a focus on amino acid sequence variation. It is based on the GLUE data-centric bioinformatics environment and provides a browsable database of amino acid replacements and coding region indels that have been observed in sequences from the pandemic. Users may also analyse their own SARS-CoV-2 sequences by submitting them to the web application to receive an interactive report containing visualisations of phylogenetic classification and highlighting genomic variation of potentially high impact, for example linked to primer mismatches.Availability and implementation Available at http://cov-glue.cvr.gla.ac.uk. Implemented using GLUE, an open source framework for the development of virus sequence data resources. Contact josh.singer@glasgow.ac.uk
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“They are frequently sensitive to mutation in these residues and select for K417N, E484K and N501Y mutations in SARS-CoV-2 S protein expression libraries in yeast and VSV 12,15,33.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [33]
In the citing paper
“Additionally, K417N, Y453F, S477R, N501Y, and D614G represent circulating variants some of which have been associated with rapidly increasing case numbers14,15,19,33–35.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [33]
In the citing paper
“A475V is resistant to class 1 antibodies (structurally defined as described29); E484K and Q493R are resistant to class 2 antibodies7,8,12,13,29,30,32,33; while R346S, N439K, and N440K are resistant to class 3 antibodies7,8,12,13,29,33.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [33]
Citations
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
An interactive web-based dashboard to track COVID-19 in real time
Dong, E., Du, H., & Gardner, L. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30120-1 · Cited by 10,048
Gorbalenya, A. E., Baker, S. C., Baric, R. S., de Groot, R. J., Drosten, C., Gulyaeva, A. A., Haagmans, B. L., Lauber, C., Leontovich, A. M., Neuman, B. W., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0695-z · Cited by 8,745
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
Amino Acid Difference Formula to Help Explain Protein Evolution
Grantham, R. L. (1974) · Science · doi:10.1126/science.185.4154.862 · Cited by 2,363
Nidovirales: Evolving the largest RNA virus genome
Gorbalenya, A. E., Enjuanes, L., Ziebuhr, J., & Snijder, E. J. (2006) · Virus Research · doi:10.1016/j.virusres.2006.01.017 · Cited by 938
A single amino acid in the PB2 gene of influenza A virus is a determinant of host range
Subbarao, K., London, W. T., & Murphy, B. R. (1993) · Journal of Virology · doi:10.1128/jvi.67.4.1761-1764.1993 · Cited by 936
Berger, S. A., Krompaß, D., & Stamatakis, A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr010 · Cited by 515
The establishment of reference sequence for SARS‐CoV‐2 and variation analysis
Wang, C., Liu, Z., Chen, Z., Huang, X., Xu, M., He, T., & Zhang, Z. (2020) · Journal of Medical Virology · doi:10.1002/jmv.25762 · Cited by 495
Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2Preprint
Korber, B., Fischer, W., Gnanakaran, S., et al. (2020) · bioRxiv · doi:10.1101/2020.04.29.069054 · Cited by 473
Human Infection with MERS Coronavirus after Exposure to Infected Camels, Saudi Arabia, 2013
Memish, Z. A., Cotten, M. L., Meyer, B., Watson, S. J., Alsahafi, A. J., Rabeeah, A. A. A., Corman, V. M., Sieberg, A., Makhdoom, H. Q., Assiri, A. M., et al. (2014) · Emerging infectious diseases · doi:10.3201/eid2006.140402 · Cited by 360
Self-citationA distinct name is needed for the new coronavirus
Jiang, S., Shi, Z., Shu, Y., Song, J., Gao, G. F., Tan, W., & Guo, D. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30419-0 · Cited by 344
Two types of amino acid substitutions in protein evolution
Miyata, T., Miyazawa, S., & Yasunaga, T. (1979) · Journal of Molecular Evolution · doi:10.1007/bf01732340 · Cited by 321
Diallo, B., Sissoko, D., Loman, N. J., Bah, H. A., Bah, H., Worrell, M. C., Conde, L. S., Sacko, R., Mesfin, S., Loua, A., et al. (2016) · Clinical Infectious Diseases · doi:10.1093/cid/ciw601 · Cited by 262
Self-citationA dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiologyPreprint
Rambaut, A., Holmes, E. C., Hill, V., O’Toole, A. N., McCrone, J., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.17.046086 · Cited by 218
Muth, D., Corman, V. M., Roth, H., Binger, T., Dijkman, R., Gottula, L. T., Gloza‐Rausch, F., Balboni, A., Battilani, M., Rihtarič, D., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-33487-8 · Cited by 196
We shouldn’t worry when a virus mutates during disease outbreaks
Grubaugh, N. D., Petrone, M. E., & Holmes, E. C. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0690-4 · Cited by 168
Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C. N., Bateman, A. G., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., et al. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa232 · Cited by 141
Self-citationReal-time digital pathogen surveillance — the time is now
Gardy, J. L., Loman, N. J., & Rambaut, A. (2015) · Genome biology · doi:10.1186/s13059-015-0726-x · Cited by 109
No evidence for distinct types in the evolution of SARS-CoV-2
MacLean, O. A., Orton, R. J., Singer, J. B., & Robertson, D. L. (2020) · Virus Evolution · doi:10.1093/ve/veaa034 · Cited by 96
Self-citationGLUE: a flexible software system for virus sequence data
Singer, J. B., Thomson, E. C., McLauchlan, J., Hughes, J., & Gifford, R. J. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2459-9 · Cited by 92
Self-citationHufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C. N., Bateman, A. G., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., et al. (2020) · Preprints.org · doi:10.20944/preprints202005.0376.v1 · Cited by 18
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Self-citationmRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312 · Cited by 1,308
Evolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutiérrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., et al. (2021) · Science · doi:10.1126/science.abf2946 · Cited by 418
Metadata
- Authors
- Singer, J., Gifford, R., Cotten, M., & Robertson, D.
- Affiliations
- MRC University of Glasgow Centre for Virus Research (GB)
- Corresponding author
- Singer, Joshua
- Venue
- Preprints.org
- Publisher
- MDPI AG
- Published
- 2020-06-18
- OpenAlex
- W3035920796
- Cited by
- 167
- References
- 25
- Citations by year
- 2025: 5 · 2024: 10 · 2023: 16 · 2022: 30 · 2021: 85 · 2020: 21
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Locations
- Preprints.org (acceptedVersion, cc-by)
- Funders
- Wellcome Trust (220977/Z/20/Z)
- UK Research and Innovation (MC_PC_19027)
- Department of Health and Social Care
- Department for International Development
- Medical Research Council (MC_PC_19027, MC UU 12014/12, COVID-19)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, genomic variation, amino acid substitutions, indels, viral genome sequence, phylogenetic classification, primer mismatch, web application, COVID-19 pandemic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
