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Roanoke's Fralin institute uses genome sequencing to look for omicron variant in Southwest Virginia

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Virginia scientists and researchers are on the lookout for the new COVID-19 variant, omicron, which was detected in the United States for the first time last week.

No cases have been found in Virginia, but the molecular diagnostics lab at the Fralin Biomedical Research Institute at Virginia Tech-Carilion is searching for the variant in Southwest Virginia.

Carla Finkielstein, director of the molecular diagnostics lab, said researchers perform mutational analysis on each positive test on samples provided to the institute. This helps with both surveillance and understanding the latest variant.

“We want to be sure that if a new variant is emerging in some part of the world, we’re protected and try to catch it as soon as possible,” she said.

The World Health Organization designated omicron as a variant of concern two weeks ago. Preliminary evidence suggests there is an increased risk of reinfection with this variant. And early data shows it could be more transmissible than previous variants — known as alpha and delta — but conclusive data is still not available.

Variants occur when a virus reproduces and makes a mistake in the new copy, called a mutation. When enough mutations have occurred, a new version of the virus is created. Sometimes these can be advantageous for the virus, such as making it more transmissible.

This happened with the delta variant, which was first discovered in India in late 2020. It now accounts for nearly all coronavirus cases in the U.S.

South African public health officials detected the omicron variant for the first time in late November.

“Thank goodness the folks in South Africa were very transparent and told the world quickly when they isolated this variant,” the Fralin Institute’s executive director, Michael Friedlander, said. “Now we’re looking for that with our whole genome sequencing and rapid mutational analysis.”

The research institute’s lab in Roanoke receives samples from health districts across Southwest Virginia and the rest of the state. They first determine whether the sample is positive or negative for COVID-19.

Positive samples are then analyzed using a rapid mutational analysis. Researchers analyze only the regions of the gene that are relevant to the variant, such as omicron, and look to see whether all mutations associated with that variant are present. Results are available in as soon as 12 hours.

Some positive samples are also selected to undergo whole genome sequencing, which can give a more complete picture of the virus with all of its mutations. Samples are selected based on different characteristics. If the patient has been sick for a long time or has had a severe case, or if the patient traveled to a particular area, the sample could be selected for further study.

Finkielstein said her lab is running between 200 and 350 whole genome sequences per week.

The sequencing can take a few days to complete, so the rapid mutational analysis is useful to provide officials with a quick result they can use in public health responses.

Labs across the country are completing genome sequencing on positive COVID-19 samples in an effort to track known variants and look out for new ones. The U.S. has lagged behind other countries in the percentage of samples it sequences, which can affect how quickly public health officials respond to and detect new variants.

Virginia is also behind some other states as well. According to data from the CDC, Virginia has sequenced 2.76% of its positive cases, but some other states have sequenced close to 9%.

Researchers and public health officials are interested in genome sequencing in order to track each COVID-19 mutation and determine which new variants may get a foothold in the region. This can help shape robust public health responses.

“The only way you can really do that in a proactive way, to be able to respond in a timely way, is to be out ahead of it,” Friedlander said. “If you wait until there’s millions of cases of omicron, and then we start analyzing for it, we’ve already missed the opportunity to do anything about it.”

The Fralin Biomedical Research Institute started performing genome sequencing after months of conducting COVID-19 testing for the state.

Finkielstein and other researchers froze positive samples and kept them in storage. The institute was interested in going back to the samples to see when mutations happened in the region. Finkielstein eventually developed the rapid mutational analysis to study the samples. The institute alerted the state about their capability to do the rapid analysis and the whole genome sequencing.

The institute was able to submit an application to the state to complete the work and be reimbursed for the millions of dollars worth of tests being done, Friedlander said. The institute shares results with the Virginia Department of Health on a daily basis.

Friedlander said researchers involved with the lab at first set aside their normal projects and jobs to volunteer their time to do the COVID-19 testing and sequencing. Cancer, brain and heart researchers came together to use their skills in molecular biology to analyze the samples.

“I really think science is a social responsibility,” Finkielstein said. “And I think it was time for some of us to step up and help our community.”

Finkielstein normally spends her days studying the effect of circadian rhythms on cancer and tumor growth. She has continued her research while also running the molecular diagnostics lab.

Friedlander said the institute received funding from Go Virginia, a business-led economic initiative, to hire full-time workers for the lab, which has freed up more researchers to continue their work.

“You prepare your whole life and this is a moment where you need to apply everything you have learned,” Finkielstein said. “I really feel like I’m contributing my knowledge as a scientist to solve an issue that is a problem in our community.”

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Alison Graham covers Roanoke County and Salem news. She’s originally from Indianapolis and a graduate of Indiana University.

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