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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
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Journal Article
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
2023
Overview
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.
The outbreak.info genomic reports provides comprehensive and detailed information about SARS-CoV-2 lineages and mutations worldwide, which facilitates near real-time genomic surveillance.
Publisher
Nature Publishing Group US,Nature Publishing Group
