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Frequently Asked Questions

FAQs for General Public

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.

Why is genomic sequencing important?

Genomic sequencing enables us to identify and characterize variant viruses, investigate how variants impact COVID-19 disease severity, and investigate how variants impact the effectiveness of vaccines and therapeutics.

Who is a part of COVIDNet?

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), University of California institutions, diagnostic Laboratories, and academic genomic sequencing experts. For a full list of COVIDNet’s partners, “click here”.

Is COVIDNet a national initiative?

COVIDNet is a state initiative established by the California Testing Task Force in collaboration with public and private California laboratories. California’s sequencing data are also used as part of national and global COVID-19 surveillance efforts.

Should I be worried when I hear about a new variant?

Not necessarily. All viruses – including SARS-CoV-2, the virus that causes COVID-19 – evolve over time. When a virus replicates or makes copies of itself, it sometimes change, or mutates, which is normal for a virus. A virus that has acquired enough significant mutations to be recognizably different from the original virus is referred to as a “variant.” Not all variants are of any consequence, but some variants are. These are identified as variants of concern and variants of interest.

What is the difference between a “Variant of Concern” and a “Variant of Interest”?

According to the US Centers for Disease Control and Prevention (CDC):

Variants of Interest (VOI)

A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

Possible attributes of a variant of interest: 

  • Specific genetic markers that are predicted to affect transmission, diagnostics, therapeutics, or immune escape
  • Evidence that it is the cause of an increased proportion of cases or unique outbreak clusters
  • Limited prevalence or expansion in the US or other countries

Variants of Concern (VOC)

A variant for which there is evidence of an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Possible attributes of variant of concern: (In addition to the possible attributes of a variant of interest)

  • Evidence of impact on diagnostics, treatments, or vaccines
    • Widespread interference with diagnostic test targets
    • Evidence of substantially decreased susceptibility to one or more class of therapies
    • Evidence of significant decreased neutralization by antibodies generated during previous infection or vaccination
    • Evidence of reduced vaccine-induced protection from severe disease
  • Evidence of increased transmissibility
  • Evidence of increased disease severity
Why are SARS-CoV-2 genetic variants named using Greek letters?

According to the World Health Organization (WHO):

  • To assist with public discussions of variants, WHO convened a group of scientists to consider easy-to-pronounce and non-stigmatizing labels for variants of concern. At the present time, this expert group has recommended using letters of the Greek alphabet (e.g., Alpha, Beta, Gamma) to label variants. These labels do not replace existing scientific names (e.g., B.1.1.7 lineage), which convey important scientific information and will continue to be used in research.
How is whole genome sequencing used to identify outbreaks?

This video from the U.S. Food and Drug Administration provides a general answer this question.

For more information and for specific examples related to SARS-CoV-2, see this toolkit from the CDC:
COVID-19 Genomic Epidemiology Toolkit | Advanced Molecular Detection (AMD)

Can I find out what the sequence or variant is for my positive COVID-19 test?

Genomic surveillance is intended to monitor community- or population-level outbreaks of disease, or to characterize the incidence and prevalence of disease. Public health departments use whole genome sequencing and variant data for public health purposes and for situational awareness of the variants in their jurisdictions.

Genomic surveillance is performed on de-identified specimens, and thus, results are not linked to individual people. Therefore, this information cannot be shared with individuals.
Source: CDC

Questions about partnering with COVIDNet? 

Learn more about available resources     

California Department of Public Health

Viral and Rickettsial Disease
Laboratory – COVIDNet

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Richmond, CA 94804

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