Genomic Sequencing - Variants FAQs
What is genomic sequencing?
The SARS-CoV-2 genome encodes instructions organized into sections, called genes, to build the virus. Scientists use a process called genomic sequencing to decode the genes and learn more about the virus. Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to predict how it might impact health. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html
Why is genomic sequencing important to public health?
Routine analysis of genetic sequence data enables Centers for Disease Control and Prevention (CDC) and its public health partners to identify and characterize variant viruses—either new ones identified here or those already identified abroad—and to investigate how variants impact COVID-19 disease severity and how variants impact the effectiveness of vaccines and therapeutics. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html
Is the SARS-CoV-2 genomic sequencing separate from the testing conducted regularly by the UO’s Monitoring and Assessment Program (MAP)?
MAP regularly conducts viral qPCR tests that identify an active infection by detecting the virus’s genetic material in a nasal swab or saliva sample. https://www.cdc.gov/coronavirus/2019-ncov/testing/diagnostic-testing.html
Genomic sequencing is a separate process in which a sample that tested positive for COVID-19 is put through additional steps to read the DNA of the virus and compare it to other published SARS-CoV-2 genome sequences.
The University of Oregon is home to the Genomics & Cell Characterization Core Facility (GC3F) which houses advanced genome sequencing capabilities and provides these resources to researchers at the University of Oregon and other leading institutions.
Are human genomes sequenced from COVID-19 tests?
The COVID-19 sequencing process performed on viral samples from UO's MAP testing does not generate any human genetic sequence information. Only the SARS-CoV-2 RNA present in these samples is sequenced. This process is highly specific to the SARS-CoV-2 genome and does not sequence human DNA. Viral genome sequences are reported to state and local public health officials, helping them understand what SARS-CoV2 variants are present in our community.
What is a variant?
A new virus variant has one or more mutations that differentiate it from the wild-type or predominant virus variants already circulating among the general population. As expected, multiple variants of SARS-CoV-2 have been documented in the United States and globally throughout this pandemic. To inform local outbreak investigations and understand the national picture, scientists compare genetic differences among viruses to identify variants and how closely they are related to each other.
https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html
A new virus variant of SARS-CoV-2 has one or more mutations that differentiate it from predominant variants already circulating among the general population. Viruses naturally develop variations through evolution, some of which emerge and disappear others of which become more common over time.
https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html
Are COVID-19 variants more contagious?
According to the CDC, some variants appear to spread more easily and quickly than other variants, which may lead to more cases of COVID-19.
https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html
Will the current COVID-19 vaccines protect against variants?
Current studies suggest that antibodies generated through vaccination with authorized vaccines protect against severe disease caused by these variants. This is being closely investigated and more studies are underway as novel variants emerge.
https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html
What can I do to protect myself against a variant?
Rigorous compliance with public health mitigation strategies suggested by the CDC, Oregon Health Authority, Lane County Public Health, and in effect at the University of Oregon, such as vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, is essential to limit the spread of the virus that causes COVID-19 and protect public health. These same practices protect against all known SARS-CoV-2 variants.
https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html
What is the UO doing to prevent the variant from spreading to students and into the community?
The UO has maintained a layered approach to COVID-19 prevention and mitigation. Strategies include rigorous testing and contact tracing programs that allow the university to identify positive cases and contacts early to move them into isolation and quarantine.
Have other variants been detected?
GC3F has completed multiple virus sequencing runs, including deidentified samples from the UO’s surveillance testing and community-based samples. The majority of recent samples have been identified as the Delta variant (B.1.617.2).
How are samples chosen for genomic testing?
All samples collected by MAP that test positive by qPCR are currently processed for genomic sequencing if a sufficient quantity of viral RNA is present in each sample.
What is the minimum quantity of viral RNA needed to make a positive sample suitable for genomic sequencing?
Samples with qPCR cycle threshold (Ct) values of 28 or lower are suitable for genomic sequencing.
Is additional genomic sequencing planned?
MAP and GC3F will continue to sequence SARS-CoV-2 genomes from all positive samples identified by the routine qPCR testing performed by MAP.
Are all positive COVID-19 samples identified through the Monitoring and Assessment Program (MAP) also tested for a variant form of the virus?
No. Only a fraction of the positive tests MAP conducts meet the criteria for genomic sequencing, which requires a high concentration of the SARS-CoV-2 virus.
Can the lab perform contact tracing on samples in which a variant is found?
The genomic sequencing is not a clinical diagnosis and testing is not linked to any individual. Samples are de-identified for analysis at the request of public health officials and results may help the research community in understanding viral evolution.