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Genomic Surveillance

What is genomic surveillance?

When SARS-CoV-2, the virus that causes COVID-19, replicates or makes copies of itself, it acquires mutations (i.e., changes) in its genome over time. These changes in the viral genetic code are typical of all viruses. A virus that has acquired enough significant mutations to be recognizably different from the original virus is referred to as a “variant.”

COVIDNet scientists use genomic sequencing to identify these changes in the genetic code. Genomic surveillance is the process of monitoring SARS-CoV-2 genomic changes over time and in different regions. Genomic surveillance provides important information to public health, such as when and where new virus variants are emerging. Genomic sequencing of SARS-CoV-2 identifies specific genetic changes which may affect how quickly the virus can spread or other important characteristics that might impact health.

​How are genomic sequences obtained?

Genomic Sequencing Journey​

testing site or home testing

An individual goes to a COVID-19 testing site to obtain a PCR test for SARS-CoV-2.
An individual can use an at-home  COVID-19 antigen test.

specimen collection

A specimen is collected from the individual for PCR testing, or the individual takes an antigen test at home.​​​

Diagnostic testing

The individual's PCR specimen is tested for SARS-CoV-2 at a diagnostic testing laboratory, or the antigen test result is immediately known when taken at home.

Test result
The COVID-19 test result is obtained. If the COVID-19 test result is:

  • positive, the specimen is sent for sequencing
  • negative, the specimen will not be sent for sequencing.

genome sequencing laboratory

A COVIDNet whole genome sequencing laboratory, such as the CDPH Viral and Rickettsial Disease Laboratory (VRDL), may receive either a positive PCR or antigen test for genomic surveillance.

specimen sequencing

The SARS-CoV-2 specimen is sequenced by a COVIDNet laboratory partner. ​

genomic  database

Genomic data are sent to the CDPH cloud database and contribute to building a state-wide view of SARS-CoV-2 (via phylogenetic trees).

These data are used by epidemiologists and other scientists to inform public health actions, decisions, and policies to protect Californians from emerging variants. COVIDNet strives to share SARS-CoV-2 genomic data in public databases to better understand this virus and add to the knowledge base at local, national, and international levels.

Why is genomic surveillance important?

Genomic sequencing, a component of genomic surveillance, is an important tool used to monitor genetic changes in SARS-CoV-2 that may significantly impact public health.

Surveillance of SARS-CoV-2 can help detect variants with the ability to:

  • Spread more quickly among people
  • Cause either milder or more severe disease in people
  • Evade natural or vaccine-induced immunity
  • Decrease the virus' susceptibility to therapeutics such as monoclonal antibodies
  • Elude detection by diagnostic tests

Genomic surveillance allows for targeted public health action by identifying the source of exposures, tracking the spread of variants, and estimating the size of outbreaks. 

Genomic Surveillance in Action

​Tracking the prevalence of variants over time

To the right is a conceptual​ graphic that indicates the prevalence of different SARS-CoV-2 variants over time. As displayed, the number of certain variants can change significantly as new variants emerge. Tracking the prevalence of variants is important to improve our understanding of how quickly variants emerge and which specific variants are circulating in our state.

variants prevalence graph

​Illustrative data only. Please see the “Additional Websites on SARS-CoV-2 Variants” section of the Resources page for access to current data.

​Simplified SARS-CoV-2 phylogenetic tree

To the right is an example i​mage of what a SARS-CoV-2 phylogenetic tree might look like. As displayed, variants continue to evolve over time.​


SARS-CoV-2 variants 

Illustrative information only. Please see the “Additional Website​s on SARS-CoV-2 Variants” section of the Resources page​​ for access to current data.​

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