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CDC Launches National Viral Genomics Consortium to Better Map SARS-CoV-2 Transmission

DNA Genotyping and Sequencing. A technician validates genetic variants identified through whole-exome sequencing. Credit: National Institutes of Health

Rapid release of open coronavirus sequence data will help guide COVID-19 public health response, drive innovation and discovery, and advance understanding of this and future pandemics

CDC has kicked off the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium, which aims to greatly expand the use of whole genome sequencing (WGS) of the COVID-19 virus.

This national network of sequencing laboratories will speed the release of SARS-CoV-2 sequence data into the public domain.

The SPHERES consortium is an ambitious effort to coordinate SARS-CoV-2 genome sequencing nationally, organizing dozens of smaller, individual efforts into a single, distributed network of laboratories, institutions and corporations. The consortium combines the expertise, technology, and resources of 40 state and local public health departments, several large clinical laboratories, and over two dozen collaborating institutions across the federal government, academia, and the private sector.

Consortium members plan to submit all useful sequence data into public repositories at the National Library of Medicine’s National Center for Biotechnology Information (NLM/NCBI), the Global Initiative on Sharing Avian Influenza Data (GISAID), and other public sequence repositories. This will help ensure that that viral sequence data from across the United States is rapidly available for public health decision making and freely accessible to researchers everywhere.

Consortium members include:

  • Federal agencies and laboratories
  • State and local public health laboratories
  • CDC Office of Advanced Molecular Detections
  • Argonne National Laboratory
  • NIAID Office of Genomics and Advanced Technology
  • National Institute of Standards and Technology (NIST)
  • National Library of Medicine’s National Center for Biotechnology Information
  • Walter Reed Army Institute of Research (WRAIR)
  • Abbott Diagnostics
  • bioMérieux
  • Color Genomics
  • Gingko Bioworks
  • IDbyDNA
  • Illumina
  • In-Q-Tel
  • LabCorp
  • One Codex
  • Oxford Nanopore Technologies
  • Pacific Biosciences
  • Qiagen
  • Quest Diagnostics
  • Verily Life Sciences
  • Baylor University
  • Cornell University
  • Fred Hutchinson Cancer Research Center
  • Mount Sinai School of Medicine
  • New York University
  • Northern Arizona University
  • University of Buffalo
  • University of California, Berkeley
  • University of California, Davis
  • University of California, Irvine
  • University of California, Los Angeles
  • University of California, San Francisco
  • University of California, Santa Cruz
  • University of Chicago
  • University of Maryland
  • University of Minnesota
  • University of Nebraska
  • University of New Mexico
  • University of Washington
  • Yale University
  • Association of Public Health Laboratories
  • Bill and Melinda Gates Foundation
  • Broad Institute
  • Chan Zuckerberg BioHub
  • J. Craig Venter Institute
  • Public Health Alliance for Genomic Epidemiology
  • Scripps Research
  • The Jackson Laboratory
  • Translational Genomics Research Institute – North
  • Walder Foundation

For the past six years, CDC’s Office of Advanced Molecular Detection program has invested in federal and state public health laboratories to expand the use of pathogen genomics and other advanced laboratory technologies for infectious disease surveillance and outbreak response. The current consortium investment aims to save lives in the SARS-CoV-2 pandemic and prepare the United States and the world for future pandemic response.

Source: CDC, adapted.

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