CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance.

Humans SARS-CoV-2 / genetics COVID-19 Genomics Mutation

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
02 09 2022
Historique:
received: 02 04 2021
revised: 13 05 2022
accepted: 13 06 2022
pubmed: 9 7 2022
medline: 15 11 2022
entrez: 8 7 2022
Statut: ppublish

Résumé

The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast. CovRadar is freely accessible at https://covradar.net, its open-source code is available at https://gitlab.com/dacs-hpi/covradar. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btac411 PMID: 35799354
pubmed: 35799354
pii: 6633303
doi: 10.1093/bioinformatics/btac411
doi:

Substances chimiques

spike protein, SARS-CoV-2 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

4223-4225

Subventions

Organisme : European Centers for Disease Control
ID : ECDC GRANT/2021/008 ECD.12222
Organisme : Bundesministerium für Bildung und Forschung
ID : 031L0175C
Organisme : Bundesministerium für Wirtschaft und Klimaschutz Daten- und KI-gestütztes Frühwarnsystem zur Stabilisierung der deutschen Wirtschaft
ID : 01MK21009E
Organisme : German Network for Bioinformatics Infrastructure
ID : 031A537B

Informations de copyright

© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Auteurs

Alice Wittig (A)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
ORCID: 0000-0002-0578-8752

Fábio Miranda (F)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0002-6823-5995

Martin Hölzer (M)

Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
ORCID: 0000-0001-7090-8717

Tom Altenburg (T)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0002-6435-4073

Jakub M Bartoszewicz (JM)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.
ORCID: 0000-0001-6893-2371

Sebastian Beyvers (S)

Department of Biology and Chemistry, Justus-Liebig-University Gießen, Gießen 35390, Germany.

Marius A Dieckmann (MA)

Department of Biology and Chemistry, Justus-Liebig-University Gießen, Gießen 35390, Germany.

Ulrich Genske (U)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.

Sven H Giese (SH)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0002-9886-2447

Melania Nowicka (M)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0002-2403-1042

Hugues Richard (H)

Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.

Henning Schiebenhoefer (H)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0002-4471-9709

Anna-Juliane Schmachtenberg (AJ)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.

Paul Sieben (P)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.

Ming Tang (M)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany.
ORCID: 0000-0002-5993-5906

Julius Tembrockhaus (J)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.

Bernhard Y Renard (BY)

Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, Potsdam 14482, Germany.
ORCID: 0000-0003-4589-9809

Stephan Fuchs (S)

Methods Development, Research Infrastructure and Information Technology (MFI), Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › CovRadar: continuously tracking and filtering...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › CovRadar: continuously tracking and filtering...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › CovRadar: continuously tracking and filtering...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › CovRadar: continuously tracking and filtering...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › CovRadar: continuously tracking and filtering...