Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
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 learned. As a component of the Platform, the SARS-CoV-2 Data Hubs enabled the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
Gueye Khadim、Zyoud Ahmad、Yuan David Yu、Knaggs Jeff、Rahman Nadim、O?ˉCathail Colman、Gr¨1ning Bj?rn、Koopmans Marion、Cochrane Guy、Papp Kriszti¨￠n、Selvakumar Sandeep、Hunt Sarah、Jayathilaka Suran、Maier Wolfgang、Waheed Zahra、Aarestrup Frank M?ller、Csabai Istvan、Hoek Maarten、Leinonen Rasko、Skiby Jeffrey Edward、Munnink Bas Oude、Mansurova Milena、Prasad Divyae、Cummins Carla、Iqbal Zamin、Ventouratou Marianna、Guly¨￠s G¨￠bor M¨￠t¨|、Nieuwenhuijse David、Gupta Dipayan、Bouquieaux Marie-Catherine、Cezard Timoth¨|e、Sokolov Alexey、Kumar Manish、Harrison Peter W.、Rinck Gabriele、Visontai D¨￠vid、St¨|ger J¨?zsef、Amid Clara、Burdett Tony、Haseeb Muhammad、Venkataraman Sundar、McKinnon Jasmine、Koliba Martin、Szarvas Judit、Thorne Ross、Worp Nathalie
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusUniversity of FreiburgErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusE?tv?s Lor¨￠nd UniversityEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusUniversity of FreiburgEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusTechnical University of DenmarkE?tv?s Lor¨￠nd UniversityErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusTechnical University of DenmarkErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusTechnical University of DenmarkErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusE?tv?s Lor¨￠nd UniversityE?tv?s Lor¨￠nd UniversityErasmus Medical CenterEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusTechnical University of DenmarkTechnical University of DenmarkEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusErasmus Medical Center
医学研究方法基础医学生物科学研究方法、生物科学研究技术
Gueye Khadim,Zyoud Ahmad,Yuan David Yu,Knaggs Jeff,Rahman Nadim,O?ˉCathail Colman,Gr¨1ning Bj?rn,Koopmans Marion,Cochrane Guy,Papp Kriszti¨￠n,Selvakumar Sandeep,Hunt Sarah,Jayathilaka Suran,Maier Wolfgang,Waheed Zahra,Aarestrup Frank M?ller,Csabai Istvan,Hoek Maarten,Leinonen Rasko,Skiby Jeffrey Edward,Munnink Bas Oude,Mansurova Milena,Prasad Divyae,Cummins Carla,Iqbal Zamin,Ventouratou Marianna,Guly¨￠s G¨￠bor M¨￠t¨|,Nieuwenhuijse David,Gupta Dipayan,Bouquieaux Marie-Catherine,Cezard Timoth¨|e,Sokolov Alexey,Kumar Manish,Harrison Peter W.,Rinck Gabriele,Visontai D¨￠vid,St¨|ger J¨?zsef,Amid Clara,Burdett Tony,Haseeb Muhammad,Venkataraman Sundar,McKinnon Jasmine,Koliba Martin,Szarvas Judit,Thorne Ross,Worp Nathalie.Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses[EB/OL].(2025-03-28)[2025-06-09].https://www.biorxiv.org/content/10.1101/2023.04.19.537514.点此复制
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