Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses-Reference-Cited by-同舟云学术

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

Published:2024-02-15 Issue:2 Volume:10 Page:
ISSN:2057-5858
Container-title:Microbial Genomics
language:en
Short-container-title:

Author:

Rahman Nadim¹^ORCID,O'Cathail Colman¹^ORCID,Zyoud Ahmad¹^ORCID,Sokolov Alexey¹^ORCID,Oude Munnink Bas²^ORCID,Grüning Björn³^ORCID,Cummins Carla¹^ORCID,Amid Clara²^ORCID,Nieuwenhuijse David F.²^ORCID,Visontai Dávid⁴,Yuan David Yu¹^ORCID,Gupta Dipayan¹^ORCID,Prasad Divyae K.²^ORCID,Gulyás Gábor Máté⁵,Rinck Gabriele¹^ORCID,McKinnon Jasmine¹^ORCID,Rajan Jeena¹^ORCID,Knaggs Jeff¹,Skiby Jeffrey Edward⁵,Stéger József⁴^ORCID,Szarvas Judit⁵^ORCID,Gueye Khadim¹^ORCID,Papp Krisztián⁴^ORCID,Hoek Maarten²,Kumar Manish¹,Ventouratou Marianna A.¹^ORCID,Bouquieaux Marie-Catherine²,Koliba Martin⁵,Mansurova Milena¹^ORCID,Haseeb Muhammad¹^ORCID,Worp Nathalie²^ORCID,Harrison Peter W.¹^ORCID,Leinonen Rasko¹^ORCID,Thorne Ross¹^ORCID,Selvakumar Sandeep¹^ORCID,Hunt Sarah¹^ORCID,Venkataraman Sundar¹^ORCID,Jayathilaka Suran¹^ORCID,Cezard Timothée¹^ORCID,Maier Wolfgang³^ORCID,Waheed Zahra¹^ORCID,Iqbal Zamin¹^ORCID,Aarestrup Frank Møller⁵^ORCID,Csabai Istvan⁴^ORCID,Koopmans Marion²^ORCID,Burdett Tony¹^ORCID,Cochrane Guy¹^ORCID

Affiliation:

1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK

2. Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands

3. University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany

4. Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary

5. Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark

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.

Publisher

Microbiology Society

Link

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001188?crawler=true&mimetype=application/pdf

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