1887

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Volume 10, Issue 2

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

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): COVID-19 , Data sharing , Emerging variants , Genomics sequencing , Open data and SARS-CoV-2
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-02-15
2024-05-10
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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
M Gen 10, 001188 (2024); https://doi.org/10.1099/mgen.0.001188
/content/journal/mgen/10.1099/mgen.0.001188
/content/journal/mgen/10.1099/mgen.0.001188
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