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Volume 10, Issue 10

The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology Open Access

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): data sharing , evolutionary biology , mutational analysis , open access and viral genomics
Funding
This study was supported by the:
  • Public Health Agency of Canada (Award N/A)
    • Principal Award Recipient: CPHLNConsortium
  • CIHR (Award N/A)
    • Principal Award Recipient: MuhammadZohaib Anwar
  • Michael Smith Health Research BC (Award N/A)
    • Principal Award Recipient: MuhammadZohaib Anwar
  • Fonds de Recherche du Québec - Santé (Award N/A)
    • Principal Award Recipient: JulieG Hussin
  • Innovation, Science and Economic Development Canada (ISED) (Award N/A)
    • Principal Award Recipient: NotApplicable
  • Digital Research Alliance of Canada (Award N/A)
    • Principal Award Recipient: VirusSeqData Portal Academic and Health Network
  • Simon Fraser University (Research Computing Group) (Award N/A)
    • Principal Award Recipient: FionaS L Brinkman
  • Ontario Genomics (Award #OGI-201)
    • Principal Award Recipient: JaredT Simpson
  • Genome Canada (Award #OGI-136)
    • Principal Award Recipient: JaredT Simpson
  • Genome Alberta (Award ACRRP-5)
    • Principal Award Recipient: MatthewA Croxen
  • US National Institutes of Health (Award #U24CA253529)
    • Principal Award Recipient: NotApplicable
  • IVADO COVID19 Rapid Response (Award #CVD19-030)
    • Principal Award Recipient: NotApplicable
  • CIHR (Award #174924)
    • Principal Award Recipient: NotApplicable
  • Genome Canada (Award #286GET)
    • Principal Award Recipient: NotApplicable
  • CIHR (Award #ARR-175622)
    • Principal Award Recipient: NotApplicable
  • Genome Canada (Award #E09CMA)
    • Principal Award Recipient: CanCOGeNConsortium
© 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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2024-10-14
2026-02-10

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The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
M Gen 10, 001293 (2024); https://doi.org/10.1099/mgen.0.001293
/content/journal/mgen/10.1099/mgen.0.001293
/content/journal/mgen/10.1099/mgen.0.001293
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