Expanding Viral Genomic Sequencing Infrastructure in the U.S.

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Influenza viruses circulate yearly, in very large numbers, and they are constantly changing; knowing what viruses are circulating and where is critical to public health decision-making. Through a cooperative agreement with the Association for Public Health Laboratories, CDC provides funding, as well as extensive training, to a network of state labs for them to do influenza sequencing.

National Influenza Reference Centers

CDC funds three state public health labs to serve as National Influenza Reference Centers (NIRCs). These include the following:

  • California Department of Public Health Viral and Rickettsial Disease Laboratory
  • New York State Department of Health (Wadsworth Center)
  • Wisconsin State Laboratory of Hygiene

Every U.S. state sends influenza virus samples to one of these three labs equipped to perform genomic sequencing. Since 2014, the NIRCs and CDC combined have provided sequencing data on nearly 60,000 influenza viruses and made that data public to better inform influenza detection, prevention, and control efforts globally. Each NIRC sequences nearly 1,000 influenza viruses per flu season and conducts viral isolation of those viruses to assist CDC in assessing vaccine relatedness and antiviral effectiveness.

Influenza Sequencing Centers

Beginning in 2021, CDC and APHL piloted the Influenza Sequencing Center (ISC) program and, as of 2024, supported six ISCs. These include the following:

  • Colorado Department of Public and Health and Environment
  • Florida Department of Public Health Laboratories
  • Hawaii State Department of Health
  • Massachusetts Department of Public Health
  • Minnesota Department of Health
  • Texas Department of State Health Services

These public health labs are being equipped to sequence approximately 500 influenza viruses each year and are strategically placed across the United States to ensure the greatest variety of viruses possible (e.g., in high-travel or metropolitan areas that are geographically diverse). ISCs share data with CDC to rapidly identify viruses that have genetic differences that may evade vaccine protection and, update seasonal flu vaccines, and ensure their ability to protect people and save lives.

Pandemic Readiness

NIRCs and ISCs serve to provide a minimum sustainable level of testing that is needed to maintain preparedness for pandemic response. In the event of a widespread novel outbreak, these labs can provide genetic characterization support for novel influenza viruses, rapidly providing more comprehensive data for the testing and development of vaccines, diagnostics, and antivirals.