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arXiv · 2405.04734

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

Erin E. Gill·Baofeng Jia·Carmen Lia Murall·Raphaël Poujol·Muhammad Zohaib Anwar·Nithu Sara John·Justin Richardsson·Ashley Hobb·Abayomi S. Olabode·Alexandru Lepsa·Ana T. Duggan·Andrea D. Tyler·Arnaud N'Guessan·Atul Kachru·Brandon Chan·Catherine Yoshida·Christina K. Yung·David Bujold·Dusan Andric·Edmund Su·Emma J. Griffiths·Gary Van Domselaar·Gordon W. Jolly·Heather K. E. Ward·Henrich Feher·Jared Baker·Jared T. Simpson·Jaser Uddin·Jiannis Ragoussis·Jon Eubank·Jörg H. Fritz·José Héctor Gálvez·Karen Fang·Kim Cullion·Leonardo Rivera·Linda Xiang·Matthew A. Croxen·Mitchell Shiell·Natalie Prystajecky·Pierre-Olivier Quirion·Rosita Bajari·Samantha Rich·Samira Mubareka·Sandrine Moreira·Scott Cain·Steven G. Sutcliffe·Susanne A. Kraemer·Yann Joly·Yelizar Alturmessov·CPHLN consortium·CanCOGeN consortium·VirusSeq Data Portal Academic·Health network·Marc Fiume·Terrance P. Snutch·Cindy Bell·Catalina Lopez-Correa·Julie G. Hussin·Jeffrey B. Joy·Caroline Colijn·Paul M. K. Gordon·William W. L. Hsiao·Art F. Y. Poon·Natalie C. Knox·Mélanie Courtot·Lincoln Stein·Sarah P. Otto·Guillaume Bourque·B. Jesse Shapiro·Fiona S. L. Brinkman
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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 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). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling 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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Erin E. Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S. Olabode, Alexandru Lepsa, Ana T. Duggan, Andrea D. Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K. Yung, David Bujold, Dusan Andric, Edmund Su, Emma J. Griffiths, Gary Van Domselaar, Gordon W. Jolly, Heather K. E. Ward, Henrich Feher, Jared Baker, Jared T. Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H. Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A. Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G. Sutcliffe, Susanne A. Kraemer, Yann Joly, Yelizar Alturmessov, CPHLN consortium, CanCOGeN consortium, VirusSeq Data Portal Academic, Health network, Marc Fiume, Terrance P. Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G. Hussin, Jeffrey B. Joy, Caroline Colijn, Paul M. K. Gordon, William W. L. Hsiao, Art F. Y. Poon, Natalie C. Knox, Mélanie Courtot, Lincoln Stein, Sarah P. Otto, Guillaume Bourque, B. Jesse Shapiro, Fiona S. L. Brinkman. 2024-05-08. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. https://arxiv.org/abs/2405.04734

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