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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

View ORCID ProfileAlice Wittig, View ORCID ProfileFábio Miranda, View ORCID ProfileMartin Hölzer, View ORCID ProfileTom Altenburg, View ORCID ProfileJakub M. Bartoszewicz, View ORCID ProfileSebastian Beyvers, Marius A. Dieckmann, View ORCID ProfileUlrich Genske, View ORCID ProfileSven H. Giese, View ORCID ProfileMelania Nowicka, View ORCID ProfileHugues Richard, View ORCID ProfileHenning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, View ORCID ProfileBernhard Y. Renard, View ORCID ProfileStephan Fuchs
doi: https://doi.org/10.1101/2021.02.03.429146
Alice Wittig
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
2Bioinformatics Unit (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Fábio Miranda
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Martin Hölzer
2Bioinformatics Unit (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Tom Altenburg
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Jakub M. Bartoszewicz
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
2Bioinformatics Unit (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Sebastian Beyvers
3Bioinformatics & Systems Biology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 58, 35390 Gießen, Germany
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Marius A. Dieckmann
3Bioinformatics & Systems Biology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 58, 35390 Gießen, Germany
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Ulrich Genske
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Sven H. Giese
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Melania Nowicka
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Hugues Richard
2Bioinformatics Unit (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Henning Schiebenhoefer
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Anna-Juliane Schmachtenberg
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Paul Sieben
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Ming Tang
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
4Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Julius Tembrockhaus
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Bernhard Y. Renard
1Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 - 3, 14482 Potsdam, Germany
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Stephan Fuchs
2Bioinformatics Unit (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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  • For correspondence: fuchss@rki.de
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ABSTRACT

The SARS-CoV-2 pandemic underlined the importance of molecular surveillance to track the evolution of the virus and inform public health interventions. Fast analysis, easy visualization and convenient filtering of the latest virus sequences are essential for this purpose. However, access to computational resources, the lack of bioinformatics expertise, and the sheer volume of sequences in public databases complicate surveillance efforts. CovRadar combines an analytical pipeline and a web application designed for the molecular surveillance of the spike gene of SARS-CoV-2, an important vaccine target. The intuitive web front-end focuses on mutations rather than viral lineages and provides easy access to frequencies and spatio-temporal distributions from global sample collections. The data is regularly updated based on a scalable and reproducible analytical back-end. With this platform, we aim to give users, those with or without bioinformatics skills or sufficient computational resources, the possibility to track and explore mutational changes in the SARS-CoV-2 spike gene and to filter, download, and further analyze data that meet their questions and needs. Advanced computational users have the ability to apply the analytical pipeline and data visualization methods locally on their own data. CovRadar is freely accessible at https://covradar.net, source code is available at https://gitlab.com/dacs-hpi/covradar.

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Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://covradar.net/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 16, 2022.
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M. Bartoszewicz, Sebastian Beyvers, Marius A. Dieckmann, Ulrich Genske, Sven H. Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. Renard, Stephan Fuchs
bioRxiv 2021.02.03.429146; doi: https://doi.org/10.1101/2021.02.03.429146
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
Alice Wittig, Fábio Miranda, Martin Hölzer, Tom Altenburg, Jakub M. Bartoszewicz, Sebastian Beyvers, Marius A. Dieckmann, Ulrich Genske, Sven H. Giese, Melania Nowicka, Hugues Richard, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Paul Sieben, Ming Tang, Julius Tembrockhaus, Bernhard Y. Renard, Stephan Fuchs
bioRxiv 2021.02.03.429146; doi: https://doi.org/10.1101/2021.02.03.429146

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