At a glance
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 to do influenza virus genomic 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 over 92,000 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 season and conducts viral isolation of a subset of those viruses. These activities help CDC assess if circulating viruses are genetically and antigenically related to strains included in influenza vaccines and that antivirals remain effective.
Influenza Sequencing Centers
Beginning in 2021, CDC and APHL piloted the Influenza Sequencing Center (ISC) program and currently supports six ISCs. These include the following:
- Colorado Department of Public and Health and Environment
- Florida Department of Public Health Laboratories
- Massachusetts Department of Public Health
- Michigan Department of Health and Human Services
- Minnesota Department of Health
- Texas Department of State Health Services
These public health labs are 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). The broader distribution of ISCs allows them to provide timely, geographically diverse sequencing capacity that is complementary to the capacity provided by NIRCs. ISCs share data with CDC to rapidly identify genetic changes in influenza viruses and inform updates to seasonal flu vaccines, ensuring their ability to protect people from influenza and save lives.
Pandemic Preparedness
NIRCs and ISCs serve a key role in pandemic preparedness and outbreak response by maintaining a sustainable sequencing infrastructure that can be scaled-up as needed. In the event of a widespread novel influenza outbreak, these labs can provide genetic characterization support to facilitate CDC’s analysis of viruses, rapidly providing more comprehensive data for the testing and development of vaccines, diagnostics, and antivirals. This system was leveraged during CDC’s 2024-2025 outbreak response to influenza A(H5) (bird flu) to sustain high-volume, timely sequencing of influenza A positive samples for enhanced disease surveillance.