Profile Picture Clint Paden

created May 24 2021

updated Feb 16 2024

Description

To identify and track SARS-CoV-2 variants, CDC uses genomic surveillance. CDC's national genomic surveillance system collects SARS-CoV-2 specimens for sequencing through the National SARS-CoV-2 Strain Surveillance (NS3) program, as well as SARS-CoV-2 sequences generated by commercial or academic laboratories contracted by CDC and state or local public health laboratories. Viral genomic sequences are analyzed and classified as a particular variant. The proportions of variants in a population are estimated nationally, by HHS region, and by jurisdiction. The thousands of sequences analyzed every week through CDC’s national genomic sequencing and bioinformatics efforts fuel this comprehensive and population-based U.S. surveillance system established to identify and monitor the spread of variants.
These data appear on the CDC COVID Data Tracker at the following URL: https://covid.cdc.gov/covid-data-tracker/#variant-proportions
For more information on how these data are generated and used to provide estimates of variant proportions, please see the following references:

  • Paul P, France AM, Aoki Y, et al. Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021. MMWR Morb Mortal Wkly Rep 2021;70:846–850. DOI: http://dx.doi.org/10.15585/mmwr.mm7023a3

  • Lambrou AS, Shirk P, Steele MK, et al. Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022. MMWR Morb Mortal Wkly Rep 2022;71:206–211. DOI: http://dx.doi.org/10.15585/mmwr.mm7106a4

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Category
Laboratory Surveillance
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Public
Tags
sars-cov-2, covid-19, surveillance, variant surveillance, variant proportion, nowcasting
Row Label
Weekly estimate of SARS-CoV-2 variant as a proportion of surveillance sequencing
SODA2 Only
Yes
Licensing and Attribution
Data Provided By
CORVD Laboratory Branch
Source Link
https://www.cdc.gov
License
Public Domain U.S. Government
Common Core
Contact Name
Clinton Paden
Contact Email
respvirus@cdc.gov
Public Access Level
public
Bureau Code
009:20
Program Code
009:026
Geographic Coverage
United States
Update Frequency
Two Weeks
Data Quality
Suggested Citation
Ma KC, Shirk P, Lambrou AS, et al. Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages — United States, January 2022–May 2023. MMWR Morb Mortal Wkly Rep 2023;72:651–656. DOI: http://dx.doi.org/10.15585/mmwr.mm7224a2
Geographic Unit of Analysis
National (USA); HHS Region
Analytical Methods Reference
https://github.com/CDCgov/SARS-CoV-2_Genomic_Surveillance
Footnotes
Lambrou AS, Shirk P, Steele MK, et al. Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022. MMWR Morb Mortal Wkly Rep 2022;71:206–211. DOI: http://dx.doi.org/10.15585/mmwr.mm7106a4; Paul P, France AM, Aoki Y, et al. Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021. MMWR Morb Mortal Wkly Rep 2021;70:846–850. DOI: http://dx.doi.org/10.15585/mmwr.mm7023a3
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