作者
Karthik Gangavarapu, Alaa Abdel Latif, Julia L Mullen, Manar Alkuzweny, Emory Hufbauer, Ginger Tsueng, Emily Haag, Mark Zeller, Christine M Aceves, Karina Zaiets, Marco Cano, Xinghua Zhou, Zhongchao Qian, Rachel Sattler, Nathaniel L Matteson, Joshua I Levy, Raphael TC Lee, Lucas Freitas, Sebastian Maurer-Stroh, GISAID Core and Curation Team, Marc A Suchard, Chunlei Wu, Andrew I Su, Kristian G Andersen, Laura D Hughes
发表日期
2023/4
期刊
Nature Methods
卷号
20
期号
4
页码范围
512-522
出版商
Nature Publishing Group US
简介
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how …
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