National SARS-CoV-2 Strain Surveillance (NS3)

Thank you for your participation to help establish the US national SARS-CoV-2 genomic surveillance system. There are multiple potential applications for routinely sequencing SARS-CoV-2 clinical isolates as part of the public health response to the COVID-19 pandemic, including population-level molecular epidemiology, outbreak investigation and virus characterization. Below please find links to download specimen submission guidance and the specimen submission form.

Guidance Documents

CDC requests that state public health laboratories provide, on a weekly basis, confirmed, deidentified diagnostic specimens to CDC to support the NS3 program. CDC prefers specimens with Ct values < 28 that have not already been sequenced. Specimens will ideally represent a variety of demographic and clinical characteristics and geographic locations. Selection of a diverse set of specimens will help ensure a representative set of sequences are generated for national monitoring.

Please see the documents below for additional details for submission guidance and shipping instructions:

Guidance for submitting SARS-CoV-2 positive samples to CDC's NS3 Program (Updated: September 26, 2023)
Appendix 2: Guidance for In-house SARS-CoV-2 sequencing (Updated: September 26, 2023)

The following documents provide information for GFAT form:

Global File Accessioning Template (GFAT) Form (Updated: September 26, 2023)
Appendix 3: GFAT Column Descriptions (Updated: September 26, 2023)

Additional Resources:

NS3 Frequently Asked Questions (Updated: September 26, 2023)
Technical Assistance for Categorizing Baseline Surveillance Guidance for In-house Sequencing (Updated: October 7, 2021)

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.

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National SARS-CoV-2 Strain Surveillance (NS3)

Guidance Documents

Questions?​​

Questions?