A national open genomics consortium for the response to emerging infectious diseases


In 2020, the Advanced Molecular Detection program established the Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium to coordinate SARS-CoV-2 sequencing. The consortium continues to monitor SARS-CoV-2 variants and other disease threats in the public health landscape and serves as a forum for knowledge and data sharing. The SPHERES collaboration includes scientists from clinical and public health laboratories, academic institutions, and the private sector.

Decorative: SPHERES logo


The SPHERES consortium is led by CDC's Advanced Molecular Detection (AMD) program, which invests in federal, state, and local public health laboratories to expand the use of pathogen genomics and other advanced laboratory technologies to strengthen infectious disease surveillance and outbreak response.

The SPHERES consortium includes over 1800 scientists from over 250 federal, state, county, local public health laboratories, several large regional and national clinical diagnostic corporations, and academic and non-profit leaders in pathogen genomics, bioinformatics, and public health from across the country. The consortium offers a unique forum for engagement across the public health, academic and private sectors to better understand the genomics and patterns of SARS-CoV-2 and other emerging infectious disease transmission across the United States.

Consortium priorities

The SPHERES consortium

  • Fosters a research community for interdisciplinary and innovative research and development in applied public health pathogen genomics, bioinformatics, and genomic epidemiology
  • Expands public health sequencing and response efforts across the United States by engaging academic and private sector laboratories
  • Improves communication and knowledge-sharing between US laboratories
  • Provides a forum to exchange information on critical data and metadata standards
  • Reduces barriers to bioinformatic analysis and data sharing
  • Aligns sequencing resource needs to technology, expertise, and other support

During the COVID-19 response‎

SPHERES accelerated the use of real-time pathogen sequence data and molecular epidemiology to provide context for SARS-CoV-2 variant surveillance data.

Consortium objectives

The SPHERES consortium’s 7 core objectives are to

  1. Establish a forum for experts from a variety of disciplines and sectors that can advance national genomic sequencing capabilities
  2. Identify and prioritize capabilities and resource needs for genomic sequencing and align to federal, non-governmental and private sector resources
  3. Improve coordination of genomic sequencing between institutions and jurisdictions and support a resilient system
  4. Accelerate data generation while championing openness, standards-based analysis, and rapid data sharing in public data repositories to address emerging infectious disease threats
  5. Provide a common forum for US public, private, and academic institutions to share protocols, methods, bioinformatics tools, standards, and best practices
  6. Develop consistent, community-led data and metadata standards, including streamlined repository submission processes, sample prioritization criteria, and a framework for shared, privacy-compliant unique case identifiers
  7. Align with other national sequencing and bioinformatics networks, and support global efforts to advance the use of standards and open data in public health

For more information

To request additional information about the SPHERES consortium, including how to join, please email CDC's Office of Advanced Molecular Detection at oamd@cdc.gov.