arXiv 2405.047342024-05-08q-bio.GN

加拿大 VirusSeq 数据门户与 Duotang：面向 SARS-CoV-2 病毒序列和基因组流行病学的开放资源

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, Alexa… 展开作者

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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AI总结：

本文介绍加拿大 VirusSeq 数据门户及 Duotang 平台，通过标准化开放数据、质量控制和交互式变异株分析，支持 SARS-CoV-2 基因组共享与公共卫生决策。

摘要：

COVID-19 大流行促使全球开展大规模工作，对来自患者样本的 SARS-CoV-2 基因组进行测序，以追踪病毒演化并为公共卫生响应提供信息。数百万条 SARS-CoV-2 基因组序列已存入全球公共存储库。Canadian COVID-19 Genomics Network（CanCOGeN - VirusSeq）是一个在大流行早期负责协调整个加拿大 SARS-CoV-2 基因组扩大测序工作的联盟；该联盟创建了 Canadian VirusSeq Data Portal，以及相关数据流程和程序，以支持这些工作。VirusSeq 的目标是开放获取加拿大 SARS-CoV-2 基因组序列以及其他存储库中无法获得的、增强且标准化的背景数据，并使这些数据符合 FAIR 原则（可发现、可访问、可互操作和可重用）。该门户的数据提交流程包含数据质量检查程序，并对数据生成者给予适当致谢，从而鼓励协作。在此，我们还重点介绍 Duotang，这是一个展示加拿大境内流行和新兴 SARS-CoV-2 变异株基因组流行病学与建模分析的网络平台。Duotang 展示加拿大及各省 SARS-CoV-2 变异株构成的动态变化，估计变异株增长，并显示互补的交互式可视化结果，同时提供当前形势的文字概述。VirusSeq Data Portal 和 Duotang 资源，以及根据该门户数据计算得到的其他分析和资源（COVID-MVP、CoVizu），均为开源且可免费获取。它们共同提供了 SARS-CoV-2 演化的最新图景，以促进科学讨论、为公共讨论提供信息，并支持与公共卫生机构之间以及公共卫生机构内部的沟通。它们也可作为一个框架，服务于其他有兴趣开展开放、协作式序列数据共享与分析的司法管辖区。

英文摘要：

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.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。