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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Karthik Gangavarapu; Alaa Abdel Latif; Julia Mullen; Manar Alkuzweny; Emory Hufbauer; Ginger Tsueng; Emily Haag; Mark Zeller; Christine M. Aceves; Karina Zaiets; Marco Cano; Jerry 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.
Affiliation
  • Karthik Gangavarapu; University of California, Los Angeles
  • Alaa Abdel Latif; The Scripps Research Institute
  • Julia Mullen; The Scripps Research Institute
  • Manar Alkuzweny; University of Notre Dame
  • Emory Hufbauer; The Scripps Research Institute
  • Ginger Tsueng; The Scripps Research Institute
  • Emily Haag; The Scripps Research Institute
  • Mark Zeller; The Scripps Research Institute
  • Christine M. Aceves; The Scripps Research Institute
  • Karina Zaiets; The Scripps Research Institute
  • Marco Cano; The Scripps Research Institute
  • Jerry Zhou; The Scripps Research Institute
  • Zhongchao Qian; The Scripps Research Institute
  • Rachel Sattler; The Scripps Research Institute
  • Nathaniel L Matteson; The Scripps Research Institute
  • Joshua I. Levy; The Scripps Research Institute
  • Raphael TC Lee; GISAID Global Data Science Initiative
  • Lucas Freitas; GISAID Global Data Science Initiative
  • Sebastian Maurer-Stroh; GISAID Global Data Science Initiative
  • - GISAID core and curation team; GISAID Global Data Science Initiative
  • Marc A. Suchard; University of California, Los Angeles
  • Chunlei Wu; The Scripps Research Institute
  • Andrew I. Su; The Scripps Research Institute
  • Kristian G. Andersen; The Scripps Research Institute
  • Laura D. Hughes; The Scripps Research Institute
Preprint in English | medRxiv | ID: ppmedrxiv-22269965
ABSTRACT
The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 10 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 and opinionated visualizations in the variant and location focussed reports 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 present a case study that illustrates 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. With an emphasis on scalability, interactivity, interpretability, and reusability, outbreak.info provides a template to enable genomic surveillance at a global and localized scale.
License
cc_by
Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2022 Document type: Preprint
Full text: Available Collection: Preprints Database: medRxiv Language: English Year: 2022 Document type: Preprint
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