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Center for laboratory sciences


The California SARS-CoV-2 Whole Genome Sequencing Initiative called COVIDNet is an unprecedented public-privat​e partnership to provide California with genomic sequencing data for epidemiological efforts to control the spread of COVID-19.

COVIDNet was establishe​d 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:​​​​​

Map of CaliforniaTrack 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 i​n 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.

virusesCharacterize 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:

  • Which variants are circulating within California?
  • 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)?​
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