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.

中文翻译：

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动员和分析公开的 SARS-CoV-2 数据以应对大流行

COVID-19 大流行引发了大规模的病原体基因组测序工作，成为监测和流行病研究工具箱的一部分。这导致开放存储库的数据共享达到前所未有的水平，积极支持了 SARS-CoV-2 结构、分子相互作用、突变和变体的识别，并促进了疫苗开发和药物再利用研究和设计。欧洲 COVID-19 数据平台的推出是为了支持这种数据共享，并已沉积了数百万个 SARS-CoV-2 原始读数。在本文中，我们描述了 (1) 开放数据共享，(2) 用于提交、分析、可视化和数据声明的工具（例如 ORCiD），(3) 通过 SARS-CoV-2 数据对这些数据集进行大规模系统分析中心以及 (4) 经验教训。本文介绍了该平台的一个组成部分，即 SARS-CoV-2 数据中心，它可以扩展和建立基础设施，我们打算在未来更广泛地使用这些基础设施来进行病原体监测和大流行病防范。