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The Canadian VirusSeq Data Portal and Duotang: Open Resources for SARS-CoV-2 Viral Sequences and Genomic Epidemiology

Microbial genomics(2024)SCI 2区

Simon Fraser Univ | McGill Univ | Montreal Heart Inst | Ontario Inst Canc Res | DNAstack | Western Univ | Publ Hlth Agcy Canada | Univ Montreal | Department of Microbiology and Immunology | Alberta Precis Labs | Canadian Ctr Computat Genom | Sunnybrook Research Institute | ECCC | Univ British Columbia | Univ Calgary

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Abstract
The COVID- 19 pandemic led to a large global effort to sequence SARS- CoV- 2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS- CoV- 2 genome sequences have been deposited in global public repositories. The Canadian COVID- 19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS- CoV- 2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS- CoV- 2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR- Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS- CoV- 2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS- CoV- 2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID- MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS- CoV- 2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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data sharing,evolutionary biology,mutational analysis,open access,viral genomics
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要点】:本文介绍了加拿大病毒序列数据门户(VirusSeq)和Duotang平台,这两个开放资源旨在提供SARS-CoV-2病毒序列和基因组流行病学信息,其创新点在于提供了增强的标准化背景数据,并符合FAIR标准,同时拥有质量控制流程和鼓励合作的机制。

方法】:通过创建数据门户和相关数据管道、程序,以及结合其他资源和分析工具,如Viral AI和Coronavirus Variants Rapid Response Network(CoVaRR-Net),来支持SARS-CoV-2基因组的广泛测序和分析。

实验】:数据门户通过一系列的数据治理原则和实践确保了符合加拿大隐私法规、数据安全标准和组织流程;Duotang平台则提供关于加拿大及各省SARS-CoV-2变异株的动态变化、增长估计和互补的互动可视化。这些资源均为开源且免费提供,便于跟踪病毒进化,支持公共卫生讨论和沟通。