Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

Autor: Rahman N; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., O'Cathail C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Zyoud A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Sokolov A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Oude Munnink B; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Grüning B; University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany., Cummins C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Amid C; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Nieuwenhuijse DF; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Visontai D; Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary., Yuan DY; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Gupta D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Prasad DK; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Gulyás GM; Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark., Rinck G; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., McKinnon J; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Rajan J; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Knaggs J; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Skiby JE; Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark., Stéger J; Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary., Szarvas J; Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark., Gueye K; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Papp K; Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary., Hoek M; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Kumar M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Ventouratou MA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Bouquieaux MC; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Koliba M; Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark., Mansurova M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Haseeb M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Worp N; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Harrison PW; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Leinonen R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Thorne R; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Selvakumar S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Hunt S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Venkataraman S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Jayathilaka S; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Cezard T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Maier W; University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany., Waheed Z; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Iqbal Z; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Aarestrup FM; Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark., Csabai I; Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary., Koopmans M; Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands., Burdett T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK., Cochrane G; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Jazyk: angličtina
Zdroj: Microbial genomics [Microb Genom] 2024 Feb; Vol. 10 (2).
DOI: 10.1099/mgen.0.001188
Abstrakt: 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.
Databáze: MEDLINE