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Rahman N, O'Cathail C, Zyoud A, Sokolov A, Oude Munnink B, Grüning B, Cummins C, Amid C, Nieuwenhuijse DF, Visontai D, Yuan DY, Gupta D, Prasad DK, Gulyás GM, Rinck G, McKinnon J, Rajan J, Knaggs J, Skiby JE, Stéger J, Szarvas J, Gueye K, Papp K, Hoek M, Kumar M, Ventouratou MA, Bouquieaux MC, Koliba M, Mansurova M, Haseeb M, Worp N, Harrison PW, Leinonen R, Thorne R, Selvakumar S, Hunt S, Venkataraman S, Jayathilaka S, Cezard T, Maier W, Waheed Z, Iqbal Z, Aarestrup FM, Csabai I, Koopmans M, Burdett T, Cochrane G. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microb Genom 2024; 10:001188. [PMID: 38358325 PMCID: PMC10926692 DOI: 10.1099/mgen.0.001188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 01/14/2024] [Indexed: 02/16/2024] Open
Abstract
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
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Affiliation(s)
- Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Bas Oude Munnink
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Björn Grüning
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Clara Amid
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | | | - Dávid Visontai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - David Yu Yuan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Divyae K. Prasad
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Gábor Máté Gulyás
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jasmine McKinnon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeff Knaggs
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeffrey Edward Skiby
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - József Stéger
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Judit Szarvas
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Khadim Gueye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Krisztián Papp
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Maarten Hoek
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marianna A. Ventouratou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Martin Koliba
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Milena Mansurova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nathalie Worp
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Peter W. Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sundar Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Timothée Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Maier
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Istvan Csabai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Marion Koopmans
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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