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COVIDNet

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.

COVIDNet Overview

What are COVIDNet’s goals?

COVIDNet has two primary goals:

Track the spread of SARS-CoV-2 in California.

A primary goal of COVIDNet is to generate the genomic sequence of SARS-CoV-2, the virus that causes COVID-19, circulating in California. These genomic sequences are used by COVIDNet scientists to construct a family tree, known as a phylogenetic tree, of the virus that illustrates how the circulating viruses are related to each other. Public health officials use these trees to determine how quickly and where the virus is spreading in California as well as to identify and track new variants of the virus to inform public health action and policies.

Characterize new cases and outbreaks using genomic data.

Genomic data help identify and distinguish cases tied to community spread, a concentrated outbreak, or a new virus introduction and will help local health officials determine where to take targeted and focused public health actions to more quickly control viral spread.

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)?

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

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.

An individual goes to a COVID-19 testing site to obtain a PCR test for SARS-CoV-2.

(Or)

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.

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).

A specimen is collected from the individual for PCR testing.

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

The individual's specimen is tested for
SARS-CoV-2 at a diagnostic testing laboratory.

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
sequencing
journey

An individual goes to a COVID-19 testing site to obtain a PCR test for the SARS-CoV-2 virus.

(Or)

An individual goes to a COVID-19 testing site to obtain a confirmatory PCR test for the SARS-CoV-2 virus after receiving a positive antigen (rapid) test result.

An individual goes to a COVID-19 testing site to obtain a PCR test for SARS-CoV-2.

(Or)

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.

A specimen is collected from the individual for PCR testing.

The individual's specimen is tested for the SARS-COV-2 virus at a diagnostic testing laboratories.

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

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 the positive SARS-CoV-2 specimen to be processed at a state processing laboratories such as the Viral and Rickettsial Disease Laboratory (VRDL).

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, which could be performed by a COVIDNet laboratories partner.  

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

Genomic data are sent to a state cloud database and contribute to building a state-wide view of the SARS-CoV-2 virus. These data are used by epidemiologists to inform public health actions, decisions, and policies to protect California from emerging variants. Genomic data are shared in public databases to contribute knowledge to local, national, and international public health communities.

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.

Tracking Variants chart.

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

Example – Simplified SARS-CoV-2 phylogenetic tree.

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.

Partners

Who are COVIDNet’s current partners?

COVIDNet has engaged many partners for genomic surveillance of SARS-CoV-2 in California.

Current partners include:

  • CDPH Viral and Rickettsial Disease Laboratory
  • CDPH Valencia Branch Laboratory
  • Alameda County
  • Contra Costa County
  • Fresno County
  • Humboldt County
  • Imperial County
  • Long Beach (City)
  • Monterey County
  • Orange County
  • Riverside County
  • Sacramento County
  • San Bernardino County
  • San Diego County
  • San Francisco County
  • San Joaquin County
  • San Luis Obispo County
  • San Mateo County
  • Santa Clara County
  • Shasta County
  • Napa-Solano-Yolo-Marin
  • Sonoma County
  • Tulare County
  • Ventura County
  • Avellino Labs
  • Avrok Laboratories
  • Chan Zuckerberg Biohub
  • Color Health
  • Curative, Inc.
  • Fulgent Genetics
  • Invitae Corporation
  • Kaiser Permanente Northern California
  • LetsGetChecked Labs
  • The Scripps Research Institute Andersen Laboratory
  • SEARCH Alliance
  • UC Berkeley Innovative Genomics Institute SARS-CoV-2
    Sequencing Team
  • UC Irvine Campus Covid Testing Laboratory & Genomics
    High Throughput Facility
  • UCLA Swab-Seq Laboratory
  • UCLA Technology Center for Genomics & Bioinformatics
  • University of California Office of the President (UCOP)
  • UC Riverside Institute for Integrative Genome Biology
    Genomics Core
  • UC San Diego EXCITE Laboratory
  • UC San Francisco Center for Advanced Technology
  • UC San Francisco Chiu Laboratory
  • Kristian Andersen
  • Patrick Ayscue
  • Sidney M. Bell
  • Shannon Bennett
  • Charles Y. Chiu
  • Russell Corbett-Detig
  • David Haussler
  • A. Marm Kilpatrick

  • Ha Youn Lee
  • Erin Mordecai
  • Julia A. Palacios
  • Joel R. Sevinsky
  • Marc A. Suchard
  • Katharine S. Walter
  • Joel Wertheim

Questions about partnering with COVIDNet? 

Learn more about available resources     

California Department of Public Health

Viral and Rickettsial Disease
Laboratory – COVIDNet

850 Marina Bay Parkway

Richmond, CA 94804

Copyright © 2021 State of California