​​​​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 Docum​​ents

State public health laboratories are requested provide, on a biweekly basis:

  1. Confirmed, deidentified, diagnostic specimens (with Ct values < 28 and not previously sequenced) and

  2. Standardized metadata on a selection of 5 COVID-19 cases.

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:​


For technical guidance on submission, interpretation or other technical sequencing related questions for SARS-CoV-2, please contact sarsseqshipping@cdc.gov.  

For shipping account information or general questions on the national sequence-based surveillance strategy for SARS-CoV-2, please contact eoc@aphl.org.