FAQ Genomic Sequencing

FAQ
Genomic Sequencing - Variants 

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 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 testing program, MAP?

MAP regularly conducts viral qPCR tests that identify an active infection by detecting the virus’s genetic material in a nasal swab 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.

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/cases-updates/variant-surveillance/genomic-surveillance-dashboard.html

https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html

What is the variant that was recently identified by sequencing at UO?

The B.1.427/B.1.429 (first identified in California) is one of many found across the U.S., and has been detected in at least 19 countries and 49 states. The CDC is monitoring variants of concern and has not yet added the California variant to its watch list at this time.

https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html

https://outbreak.info/situation-reports?country=United%20States&division=California&pango=B.1.429&selected=United%20States&selectedType=country

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

How did the variant make it to Lane County?

Multiple variants of the SARS-CoV-2 virus have been found in communities across Oregon. The B.1.427/B.1.429 variant was first detected last summer in Southern California and now has been documented in 49 states and 19 countries.

Will the current COVID-19 vaccine protect against variants?

Current studies suggest that antibodies generated through vaccination with authorized vaccines recognize these variants. This is being closely investigated and more studies are underway.

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 other students and into the community?

The UO has maintained a rigorous testing and contact tracing program that allows 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. None of the sequencing samples, as of March 1, 2021, have been variants of concern, as defined by the CDC. 

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.