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

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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Publication Details

Journal
Microbial Genomics
Published
2024-10-14
DOI
https://doi.org/10.1099/mgen.0.001293
Citations
3
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
1.17

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article

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

Sandrine Moreira, Ana T. Duggan, Jared T. Simpson, Art F. Y. Poon et al.
3 citations
Microbial Genomics
SARS-CoV-2 and COVID-19 Research
1.17
article

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

Sandrine Moreira, Ana T. Duggan, Jared T. Simpson, Art F. Y. Poon, Susanne A. Kraemer, Mélanie Courtot, Gary Van Domselaar, Jaser Uddin, Natalie Prystajecky, Christina K. Yung, Matthew A. Croxen, Julie Hussin, Yann Joly, Dusan Andric, William Hsiao, Abayomi S. Olabode, Emma Griffiths, Baofeng Jia, Raphaël Poujol, Alexandru Lepsa, Paul M. K. Gordon, Kim Cullion, José Héctor Gálvez, Muhammad Zohaib Anwar, Arnaud N’Guessan, Leonardo Landa Rivera, Samantha Rich, Jiannis Ragoussis, Scott Cain, Guillaume Bourque, Samira Mubareka, Fiona S. L. Brinkman, Jeffrey B. Joy, Lincoln Stein, Gordon Jolly, Pierre-Olivier Quirion, David Bujold, Jared Baker, B. Jesse Shapiro, Terrance P. Snutch, Steven G. Sutcliffe, Nithu Sara John, Catalina López-Correa, Rosita Bajari, Sarah Perin Otto, Natalie Knox, Brandon Chan, Ashley E. Hobb, Cindy Bell, Erin E. Gill, Carmen Lía Murall, Caroline Colijn, Heather Ward, Karen Fang, Atul Kachru, Henrich Feher, Jon Eubank, Mitchell Shiell, Yelizar Alturmessov, Justin Richardsson, Qian Xiang, Andrea D. Tyler, Jörg H. Fritz, Marc Fiume, Catherine Yoshida, Edmund Su
article en
3 citations

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.

Microbial GenomicsVol. 10(10)
Ontario Institute for Cancer Research (CA), Western University (CA), Sunnybrook Health Science Centre (CA), University of British Columbia (CA), University of Alberta (CA), University of Calgary (CA), Public Health Agency of Canada (CA), Simon Fraser University (CA), University of Toronto (CA), Montreal Heart Institute (CA), Ontario Genomics (CA), Genome Canada (CA), BC Centre for Disease Control (CA), Michael Smith Health Research BC (CA), McGill Genome Centre (CA), Women and Children’s Health Research Institute (CA), AIDS Vancouver (CA), Indoc Research (CA), Mila - Quebec Artificial Intelligence Institute (CA), McGill University (CA), Université de Montréal (CA)
Canarie, Genome Canada, Public Health Agency of Canada, Innovation, Science and Economic Development Canada, Ontario Genomics, Government of Ontario, Government of Canada, Michael Smith Health Research BC, Public Health Agency, Simon Fraser University, Genome Alberta, Institut de Valorisation des Données, Alliance de recherche numérique du Canada, National Institutes of Health, Canadian Institutes of Health Research, Fonds de Recherche du Québec - Santé
Good health and well-being
Openalex Percentile: Top 21%
SARS-CoV-2 and COVID-19 Research
1.17
DOIOpen Access PDFOpenAlex
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