The California SARS-CoV-2 Whole Genome Sequencing Initiative called COVIDNet is an unprecedented public-private partnership to provide California with genomic sequencing data for epidemiological efforts to control the spread of COVID-19.
COVIDNet was established by the California Testing Task Force as a collaborative effort between the California Department of Public Health (CDPH) and others including the Chan Zuckerberg Biohub; Local Public Health Laboratories (LPHLs); The University of California (UC) and other academic institutions; diagnostic Laboratories; and academic experts in molecular evolution, genomic epidemiology, and pathogen phylogenetics.
What are COVIDNet’s goals?
COVIDNet has two primary goals:
COVIDNet’s genomic epidemiology efforts may help answer questions such as these:
- Are certain variants of SARS-CoV-2 associated with more severe illness?
- Are emerging variants associated with increased transmission or virulence?
- Are infections in occupational settings reflective of workplace transmissions or transmissions from the surrounding community?
- Are certain variants becoming more prevalent over time?
- Are variants acquiring mutations that can escape immunity over time (e.g., infecting people who are vaccinated)?
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?
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.
An individual goes to a COVID-19 testing site to obtain a PCR test for SARS-CoV-2.
An individual goes to a COVID-19 testing site to obtain a confirmatory PCR test for SARS-CoV-2 after receiving a positive antigen (rapid) test result.
A specimen is collected from the individual for PCR testing.
The individual’s specimen is tested for SARS-CoV-2 at a diagnostic testing laboratory.
The COVID-19 PCR test result is obtained. If the COVID-19 PCR test result is:
- positive, the specimen is sent for sequencing
- negative, the specimen will not be sent for sequencing.
The diagnostic testing laboratories send positive SARS-CoV-2 specimens to be processed at a COVIDNet laboratory, such as the CDPH Viral and Rickettsial Disease Laboratory (VRDL).
The SARS-CoV-2 specimen is sequenced by a COVIDNet laboratory partner.
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.
Genomic Surveillance in Action
Tracking the prevalence of variants over time
This 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.
Illustrative information 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
This is an example image of what a SARS-CoV-2 phylogenetic tree might look like. As displayed, variants continue to evolve over time.
Who are COVIDNet’s current partners?
COVIDNet has engaged many partners for genomic surveillance of SARS-CoV-2 in California.
Current partners include:
Questions about partnering with COVIDNet?
Learn more about available resources