The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
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| Format: | Preprint |
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2024
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| author | 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. Joly, Yann Alturmessov, Yelizar consortium, CPHLN consortium, CanCOGeN Academic, VirusSeq Data Portal network, Health 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. |
| author_facet | 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. Joly, Yann Alturmessov, Yelizar consortium, CPHLN consortium, CanCOGeN Academic, VirusSeq Data Portal network, Health 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. |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_04734 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology 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. Joly, Yann Alturmessov, Yelizar consortium, CPHLN consortium, CanCOGeN Academic, VirusSeq Data Portal network, Health 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. Genomics 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. |
| title | The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology |
| topic | Genomics |
| url | https://arxiv.org/abs/2405.04734 |