Tracking omicron: A look inside a Shelby County sequence testing lab

Published: Dec. 2, 2021 at 4:58 PM CST
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MEMPHIS, Tenn. (WMC) - The work is on to identify any cases of the omicron variant in the Mid-South. States are relying on sequence testing to spot the variant, and one of the most robust programs is in Memphis.

Scientists doing sequence testing in Shelby County are looking at about 20% of all positive COVID-19 tests.

They’re looking for signs of any new variants. Doctors and government officials count on this testing to help them intervene to help reduce the variant’s transmission as soon as possible.

Action News 5 got to go inside one of those sequence testing labs to see how it’s all done.

From start to finish, sequence testing takes about two days. At a lab at the University of Tennessee Health Science Center two graduate students were starting the process on Thursday of extracting the RNA, or the virus’ genetic material, from positive COVID tests.

“We’re isolating that RNA and reading it one by one,” UTHSC Professor of Virology Dr. Colleen Jonsson said. “When we get to regions like the spike protein we look for signatures of Alpha, Beta, Gamma. Now we’re looking for the signature of omicron.”

Jonsson is director of the school’s Regional Biocontainment Laboratory and has been sequence testing viruses for years.

She and her team were able to jump in with little lag time sequencing the coronavirus at the start of the pandemic and they haven’t stopped.

“That provided actually a history,” Dr. Jonsson said.

Jonsson said after first discovering the Alpha and Delta variants it took about two months before they became the dominant strains in Shelby County.

“If omicron is the dominant sequence in two months we’ll know it’s as good as delta based just on a simple amount of time,” Dr. Jonsson said. “If it’s faster we’re probably going to appreciate that it’s more infectious.”

A COVID-19 test only tells you whether you’re positive for the virus, not the specific strain. Public health officials look to sequence testing to know the big picture of what the community is facing.

“The delta variant is still very much prevalent in our community,” Shelby omounty Health Department Director Dr. Michelle Taylor said “Our labs are on the look out of any sequencing of omicron in our community.”

The lab at UTHSC is one of a few labs doing the testing and reporting findings to county public health officials.

Arkansas and Mississippi are also relying on sequence testing to spot the omicron variant, which, as of Thursday, has been reported in three cases in the United States.

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