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Genomic Surveillance for SARS-CoV-2 Variants

Genomic Surveillance for SARS-CoV-2 Variants

Viruses are constantly changing, and this includes SARS-CoV-2, the virus that causes COVID-19. These genetic variations occur over time and can lead to the emergence of new variants that may have different characteristics.

The SARS-CoV-2 genome encodes instructions organized into sections, called genes, to build the virus. Scientists use a process called genomic sequencing to decode the genes and learn more about the virus. Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to better understand how it might impact health.

For example, some variant viruses are of particular concern because they spread easier, cause more severe disease, or may escape the body’s immune response.

As CDC and public health partners sequence more SARS-CoV-2 genomes, we will improve our understanding of which variants are circulating in the US, how quickly variants emerge, and which variants are the most important to characterize and track in terms of health.

SARS-CoV-2 genome

Genes in the SARS-CoV-2 genome that contain instructions to build parts of the virus are shown in different colors. For example, the brown section in the picture has genetic instructions to build the spike protein, which then allows the virus to attach to human cells during infection. This section of the genome serves as a key region for monitoring mutations.

SARS-CoV-2 genome

Genes in the SARS-CoV-2 genome that contain instructions to build parts of the virus are shown in different colors. For example, the brown section in the picture has genetic instructions to build the spike protein, which then allows the virus to attach to human cells during infection. This section of the genome serves as a key region for monitoring mutations.

Viruses are constantly changing, and this includes SARS-CoV-2, the virus that causes COVID-19. These genetic variations occur over time and can lead to the emergence of new variants that may have different characteristics.

The SARS-CoV-2 genome encodes instructions organized into sections, called genes, to build the virus. Scientists use a process called genomic sequencing to decode the genes and learn more about the virus. Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to better understand how it might impact health.

For example, some variant viruses are of particular concern because they spread easier, cause more severe disease, or may escape the body’s immune response.

As CDC and public health partners sequence more SARS-CoV-2 genomes, we will improve our understanding of which variants are circulating in the US, how quickly variants emerge, and which variants are the most important to characterize and track in terms of health.

How do variants occur?

genome-envelope

The virus genome is packed inside an envelope that contains proteins, including the spike protein.

Mutations are changes in the genetic code of a virus that naturally occur over time when an animal or person is infected. While a certain amount of genetic variation is expected to occur as SARS-CoV-2 spreads, it’s important to monitor circulating viruses for key mutation(s) that happen in important regions of the genome. Many mutations do not affect the virus’s ability to spread or cause disease because they do not alter the major proteins involved in infection; eventually these are outcompeted by variants with mutations that are more beneficial for the virus.

To find more information about the mutations and variants CDC is monitoring in the US and globally, go to the SARS-CoV-2 Variants page.

How do variants occur?

Mutations are changes in the genetic code of a virus that naturally occur over time when an animal or person is infected. While a certain amount of genetic variation is expected to occur as SARS-CoV-2 spreads, it’s important to monitor circulating viruses for key mutation(s) that happen in important regions of the genome. Many mutations do not affect the virus’s ability to spread or cause disease because they do not alter the major proteins involved in infection; eventually these are outcompeted by variants with mutations that are more beneficial for the virus.

To find more information about the mutations and variants CDC is monitoring in the US and globally, go to the SARS-CoV-2 Variant page.

genome-envelope

The virus genome is packed inside an envelope that contains proteins, including the Spike protein.

What is CDC doing to track SARS-CoV-2 variants?

In the United States, CDC tracks emerging variants through genomic surveillance with the following approaches:

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Leading the National SARS-CoV-2 Strain Surveillance (NS3) system

Since November 2020, CDC regularly receives SARS-CoV-2 samples from state health departments and other public health agencies for sequencing, further characterization, and evaluation. On January 25, 2021, the NS3 system was scaled-up to process 750 samples per week. Notable strength of this system is the regular collection of numerous representative specimens from across the country and characterization of viruses beyond what sequencing alone can provide.

NS3 Submission Guidance Documentsexternal icon

NS3 samples displayed as phylogenic treesexternal icon

Published COVID-19 Sequences

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Partnering with commercial diagnostic laboratories

CDC is contracting with large commercial diagnostic labs to sequence samples across the United States. CDC has commitments from these laboratories to sequence 6,000 samples per week, with the capacity to scale up in response to the nation’s needs.

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Collaborating with universities

CDC has contracts with seven universities to conduct genomic surveillance research in collaboration with public health agencies. The studies are meant to provide deeper insights into viral genomics and molecular epidemiology within the various regions across the country.

CDC awards nearly $9 million for SARS-CoV-2 Sequencing

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Supporting state, territorial, local and tribal health departments

Since 2014, CDC’s Advanced Molecular Detection Program has been integrating next-generation sequencing and bioinformatics capabilities into the U.S. public health system. Several state and local health departments have been applying these resources as part of their response to COVID-19. Public health departments support local investigations, conduct studies, and make genomic data available to public databases. To further support these efforts, on December 18, 2020, CDC released $15 million from COVID supplemental funds through the Epidemiology and Laboratory Capacity Program.

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Leading the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) consortium

Since early in the pandemic, CDC has led a national consortium of laboratories sequencing SARS-CoV-2 (SPHERES). The SPHERES consortium consists of more than 160 institutions, including academic centers, industry, non-governmental organizations, and public health agencies. Through this coordination, genomic data are made available through public databases for use by public health professionals, researchers, and industry.

Why is genomic surveillance important for public health?

  • Ability to spread more quickly in people
  • Ability to cause either milder or more severe disease in people
  • Ability to evade detection by specific diagnostic tests 
    Many commercial nucleic acid amplification tests (NAATs) that use reverse transcription polymerase chain reaction (RT-PCR) have multiple targets to detect the virus, such that even if a mutation impacts one of the targets, the other RT-PCR targets will still work. However, there are some tests that rely on only one target, and mutations may impact their ability to work. FDA is using public health sequencing data to monitor mutations and their impact on confidential/proprietary diagnostic test designs.
  • Decreased susceptibility to medical therapies that employ monoclonal antibodies
    Such therapy involves specifically designed antibodies that target regions of the virus to block infection. Because these treatments are more specific than natural immune response-generated antibodies, they may be less effective against variants that emerge.
  • Ability to evade natural or vaccine-induced immunity 
    Both natural infection with and vaccination against SARS-CoV-2 produce a “polyclonal” antibody response that targets several parts of the spike protein. The virus would need to accumulate significant mutations in the spike protein to evade immunity induced by vaccines or by natural infection.

Among these possibilities, the ability to evade vaccine-induced immunity would be the most concerning. There is no definitive evidence yet that this is occurring, but scientists are closely evaluating this possibility.