The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
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Gill Erin E, Jia Baofeng, Murall Carmen Lia, Poujol Raphaël, Anwar Muhammad Zohaib, John Nithu Sara, Richardsson Justin, Hobb Ashley, Olabode Abayomi S, Lepsa Alexandru, Duggan Ana T, Tyler Andrea D, N'Guessan Arnaud, Kachru Atul, Chan Brandon, Yoshida Catherine, Yung Christina K, Bujold David, Andric Dusan, Su Edmund, Griffiths Emma J, Van Domselaar Gary, Jolly Gordon W, Ward Heather K E, Feher Henrich, Baker Jared, Simpson Jared T, Uddin Jaser, Ragoussis Jiannis, Eubank Jon, Fritz Jörg H, Gálvez José Héctor, Fang Karen, Cullion Kim, Rivera Leonardo, Xiang Linda, Croxen Matthew A, Shiell Mitchell, Prystajecky Natalie, Quirion Pierre-Olivier, Bajari Rosita, Rich Samantha, Mubareka Samira, Moreira Sandrine, Cain Scott, Sutcliffe Steven G, Kraemer Susanne A, Alturmessov Yelizar, Joly Yann, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Fiume Marc, Snutch Terrance P, Bell Cindy, Lopez-Correa Catalina, Hussin Julie G, Joy Jeffrey B, Colijn Caroline, Gordon Paul M K, Hsiao William W L, Poon Art F Y, Knox Natalie C, Courtot Mélanie, Stein Lincoln, Otto Sarah P, Bourque Guillaume, Shapiro B Jesse, Brinkman Fiona S L
Аннотация
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.