CDC launches national viral genomics consortium to better map SARS-CoV-2 transmission

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.

The SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium, which will greatly expand the use of whole genome sequencing (WGS) of the COVID-19 virus.  Consortium members include Northern Arizona University, TGen, and the State of Ariona.

CDC Press Release

Friday, May 1, 2020

CDC has kicked off the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium, which will 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.

SPHERES will provide consistent, real-time sequence data to the public health response teams investigating cases and clusters of COVID-19 across the country. It will help them better understand how the virus is spreading, both nationally and in their local communities. Better data, in turn, will help public health officials interrupt chains of transmission, prevent new cases of illness, and protect and save lives.

“The U.S. is the world’s leader in advanced rapid genome sequencing. This coordinated effort across our public, private, clinical, and academic public health laboratories will play a vital role in understanding the transmission, evolution, and treatment of SARS-CoV-2. I am confident that our finest, most skilled minds are working together to help us save lives today and tomorrow,” said CDC Director Robert Redfield, M.D.

Tracking the COVID-19 virus as it evolves

Genomic sequence data can give unprecedented insight into the biology of SARS-CoV-2, the virus that causes COVID-19, and help define the changing landscape of the pandemic. By sequencing viruses from across the United States, CDC and other public health authorities can monitor important changes in the virus and use this information to guide contact tracing, public health mitigation efforts, and infection control strategies.

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.

SPHERES will establish best practices and consensus data standards, accelerate open data sharing, and establish a pool of resources and expertise to help bring cutting-edge technology to the national COVID-19 response.

SPHERES data: open, shared

Consortium members share a commitment to rapid open sequence sharing. They 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

  • Centers for Disease Control and Prevention, Office of Advanced Molecular Detections
  • Argonne National Laboratory
  • National Institute of Allergy and Infectious Diseases, Office of Genomics and Advanced Technology
  • National Institute of Standards and Technology
  • National Library of Medicine’s National Center for Biotechnology Information
  • Walter Reed Army Institute of Research

State/local public health laboratories

  • Arizona
  • California
  • Delaware
  • District of Columbia
  • Florida
  • Hawaii
  • Massachusetts
  • Maine
  • Maryland
  • Michigan
  • Minnesota
  • North Carolina
  • New Mexico
  • North Dakota
  • Nevada
  • New York
  • Utah
  • Virginia
  • Washington
  • Wisconsin
  • Wyoming

Academic Institutions

  • 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


  • Abbott Diagnostics
  • bioMérieux
  • Color Genomics
  • Gingko Bioworks
  • IDbyDNA
  • In-Q-Tel
  • LabCorp
  • One Codex
  • Oxford Nanopore Technologies
  • Pacific Biosciences
  • Qiagen
  • Quest Diagnostics
  • Verily Life Sciences

*Names of corporations are provided for information purposes only, and their inclusion here does not constitute an endorsement of the corporations or any of their commercial products or services by the U.S. Centers for Disease Control and Prevention.

Non-profit public health or research institutes

  • 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.

To learn more about genomic sequencing or CDC’s work in advanced molecular detection, visit


CDC works 24/7 protecting America’s health, safety and security. Whether disease start at home or abroad, are curable or preventable, chronic or acute, or from human activity or deliberate attack, CDC responds to America’s most pressing health threats. CDC is headquartered in Atlanta and has experts located throughout the United States and the world.

Posted in AZBio News, COVID-19 News and Info.