The National SARS-CoV-2 Strain Surveillance (NS3) program provides a comprehensive surveillance system for the United States to track virus evolution over time and identify emerging variants that may affect the performance of diagnostics, therapeutics, or vaccines, or that impact the transmissibility of SARS-CoV-2 or severity of COVID-19. A notable strength of NS3 is the regular collection of specimens from across the United States to support variant characterization efforts, which provides important data to inform public health decision-making. The NS3 program is dependent on jurisdictions for the shipment of culturable viral specimens to CDC and high quality, rapid sequencing and submission of sequence data to public repositories for relevant and timely data on circulating SARS-CoV-2 strains. 

NS3 Guidance Documents

The following documents provide information for GFAT form:​

Additional NS3 Resources:

NS3 Questions?​​

  • For technical guidance on submission, interpretation or other technical sequencing related questions for SARS-CoV-2, please contact sarsseqshipping@cdc.gov.  
  • For general questions on the national sequence-based surveillance strategy for SARS-CoV-2, please contact infectious.diseases@aphl.org.​

Other General Respiratory Virus Surveillance Resources


Additional respiratory virus documents are available for RSV​ and Influenza.