Paper

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

Worp, Nathalie, Amid, Clara, Haseeb, Muhammad, Zyoud, Ahmad, Ventouratou, Marianna, Harrison, Peter W., Thorne, Ross, Szarvas, Judit, Csabai, Istvan, Knaggs, Jeff, Rahman, Nadim, Gupta, Dipayan, Stéger, József, Waheed, Zahra, Gueye, Khadim, Koliba, Martin, Cezard, Timothée, Maier, Wolfgang, Grüning, Björn, Cummins, Carla, Selvakumar, Sandeep, Rinck, Gabriele, Nieuwenhuijse, David, Rajan, Jeena, Munnink, Bas Oude, Visontai, Dávid, Skiby, Jeffrey Edward, Hunt, Sarah, Koopmans, Marion, Leinonen, Rasko, Burdett, Tony, Gulyás, Gábor Máté, Venkataraman, Sundar, Aarestrup, Frank Møller, Iqbal, Zamin, Cochrane, Guy, Sokolov, Alexey, Kumar, Manish, Papp, Krisztián, Jayathilaka, Suran, Mansurova, Milena, Bouquieaux, Marie-Catherine, Prasad, Divyae, McKinnon, Jasmine, Yuan, David Yu, O’Cathail, Colman, Hoek, Maarten

2023

Overview

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.

• Publisher: Cold Spring Harbor Laboratory
• Subject: Bioinformatics