National SARS-CoV-2 Strain Surveillance (NS3)

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. 

Guidance Documents

• National SARS-CoV-2 Strain Surveillance (NS3) System Guide for Public Health Laboratories  (Updated: September 18, 2024​​)

• EXECUTIVE SUMMARY: National SARS-CoV-2 Strain Surveillance (NS3) System Guide for Public Health Laboratories
    ​(Updated: September 18, 2024)​​
  

The following documents provide information for GFAT form:​

• Global File Accessioning Template (GFAT) Form​ (Updated: February 5, 2025)​​
  

• Appendix 3: GFAT Column Descriptions (Updated: September 18, 2024)​

Additional Resources:

• Table 1: SARS-CoV-2 Bi-Weekly Sequencing and Specimen Submission Goals by Jurisdiction  (Updated: September 18, 2024)
  

• Appendix 1: Technical Assistance for Categorizing Sequence Data as Baseline Surveillance (Updated: September 18, 2024)

• Appendix 2: Shipping SARS-CoV-2 Specimens to CDC  (Updated: September 18, 2024)
  

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.​

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