What to know
In the United States, CDC uses genomic surveillance to track emerging SARS-CoV-2 variants of the virus that causes COVID-19.
Genomic surveillance is important for public health
A comprehensive system for SARS-CoV-2 genomic surveillance is important because:
- Mutations (nucleotide substitutions) occur in viruses and accumulate with continued viral spread. These mutations result in variants that may have different traits. Genomic surveillance identifies circulating variants to rapidly inform public health response efforts.
- Testing, treatment, and vaccines can be optimized for currently circulating and emerging variants.
- Detection of new variants supports outbreak preparedness and prevention efforts and strengthens public health response.
CDC tracks SARS-CoV-2 variants
CDC established multiple pipelines to connect genomic sequence data from CDC, public health laboratories, as well as academic, commercial testing, non-profit, and medical laboratories within publicly accessible databases maintained by the .
As part of the CDC National SARS-CoV-2 Strain Surveillance (NS3) System, public health laboratories ship de-identified specimens to CDC to provide a representative set of viruses for sequencing and laboratory characterization.
Genomic sequencing process for SARS-CoV-2*
There are four main stages to generating SARS-CoV-2 genetic sequence data from specimens to make it available in public repositories:
- Specimen receipt and initial processing: Clinical specimens, such as nasal swabs, are received and entered into the laboratory information system.
- Specimen preparation and sequencing: SARS-CoV-2 RNA is extracted and converted to complimentary DNA, prepared for sequencing, and loaded into the next-generation sequencing equipment.
- Sequence data generation and collection: Specimens are sequenced, and data is collected from sequencers and initial quality control steps are taken. The raw data is processed and turned into sequence data. At this point, a parallel process begins where sequence data collected from non-public health laboratories are integrated with CDC databases for processing.
- Sequence data submission to public repositories: Scientists conduct additional quality control steps. Sequences not initially accepted by public repositories are analyzed and potentially re-sequenced for resubmission. Published data are made available to scientists around the world through public repositories.
*There are quality control tests at multiple stages of the pipeline to verify the accuracy of genomic sequencing data.
Bioinformatic analysis of genomic sequence data
Public health laboratories, medical laboratories, commercial testing laboratories, research laboratories, and universities submit data directly to public repositories. CDC regularly collects and generates genomic sequence data from multiple sources to support national surveillance. Scientists at CDC conduct detailed analyses of the sequence data to identify variants and actively monitor which variants are most common in the U.S. These data are used to evaluate potential impacts on critical COVID-19 countermeasures, including testing, treatment, and vaccines.
The National SARS-CoV-2 Strain Surveillance (NS3) system
The NS3 program collects, analyzes, and shares information about the genetic diversity of SARS-CoV-2. The 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 testing, treatment, or vaccines. It can also measure the impact of the transmissibility of SARS-CoV-2 or its ability to spread.
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.
Through partnerships with public health laboratories, CDC receives specimens from jurisdictions for sequencing and further characterization of representative viruses. The NS3 program has two main goals:
- National virus monitoring: US public health laboratories send representative SARS-CoV-2–positive clinical specimens to CDC to support federal efforts to sequence, genetically analyze, and characterize viruses in the lab which have been circulating in the population over time. This also supports a repository of public SARS-CoV-2 sequence data and specimens.
- Virus characterization: Based on genomic analyses, SARS-CoV-2 variants are isolated from positive specimens provided by US public health laboratories. These isolated viruses are evaluated in CDC laboratories to understand their potential impact on current testing, treatment, vaccines, and their overall risk to public health.
As laboratories have scaled up sequencing capacity, CDC works to improve and build additional technical infrastructure and workflows to ensure efficient sequence data submission to public repositories, which store publicly accessible sequence data for scientists to include in analyses.
Next-generation sequencing is a multi-step process that involves both laboratory and bioinformatic workflows. The time from receiving a specimen at CDC to having an assembled sequence ready for submission to public databases is approximately 10 or more days. A similar timeline often applies to state, local, academic, and commercial partners. However, due to additional specimen logistics prior to sequencing, time from collection to reporting is longer.
The genetic sequence data generated by CDC and state and local public health laboratories are submitted to open-access databases.
Supporting state, territorial, local, and tribal health departments
Since 2014, CDC’s Advanced Molecular Detection program has integrated next-generation sequencing and bioinformatics capabilities into the US public health system. Many state and local health departments use genomic sequencing to monitor SARS-CoV-2.
Sequencing conducted by public health departments can help provide a better understanding of local epidemiology and transmission. These data can help investigate outbreaks of COVID-19 in various settings, such as healthcare facilities. State and federal public health agencies support local investigations, conduct studies, and make genomic data available to public databases.
Virus characterization
CDC analyzes the available genomic sequence data and provides regular updates on circulating variants on the CDC Surveillance and Data Analytics web page.
These analyses drive the selection and prioritization of a subset of representative viruses for further characterization. Virus characterization may include:
- evaluation of the ability of antibodies generated after a previous infection or vaccination to neutralize circulating viruses.
- assessment of the susceptibility of viruses to authorized treatments.
- laboratory studies to assess virus transmissibility and pathogenesis (how COVID-19 develops).
Virus isolates are shared with public health, academic, federal, and commercial partners through .