Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Top Cited Papers
- 23 February 2023
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 20 (4), 512-522
- https://doi.org/10.1038/s41592-023-01769-3
Abstract
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 outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.Keywords
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Funding Information
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (U19 AI135995, U19 AI135995-04S3, U19 AI135995-03S2, U01AI151812, U19 AI135995, U19 AI135995-04S3, U19 AI135995-03S2, U01AI151812, R01 AI162611, R01 AI153044, U19 AI135995, U19 AI135995, U19 AI135995-04S3, U19 AI135995, U19 AI135995, U01AI151812, U19 AI135995, U19 AI135995-04S3, U19 AI135995-03S2, U19 AI135995, U19 AI135995, U19 AI135995, U19 AI135995-04S3, U19 AI135995, U01AI151812)
- U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (U24 TR002306, UL1TR002550, U24 TR002306, UL1TR002550)
- U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (75D30120C09795, 75D30120C09795, 75D30120C09795)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM083924, R01GM083924)
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