Strain found in Shelby County is UK variant, UTHSC says

By , Daily Memphian Updated: February 03, 2021 9:30 AM CT | Published: February 02, 2021 12:13 PM CT

A highly suspicious sample of COVID-19 found in Shelby County is the UK variant strain B.1.1.7, according to University of Tennessee Health Science Center officials.

The sample was sequenced in the regional biocontainment lab on campus and has been sent to Nashville for confirmation.

“The hamburger is already made; they are just putting a little ketchup on it,” said Dr. Scott Strome, executive dean of the University of Tennessee Medical School. “We have a UK variant.”

The sample has the genetic markers that match the variant. It was detected in one of local labs. 

For weeks, Colleen Jonsson, head of the biocontainment lab, has been sequencing 100-plus samples of virus specimens from test sites across the city, looking for variants, particularly the four most contagious strains, including the UK strain.

By March, Dr. Jon McCullers expects a considerable levels of the variant will be here.

“We are seeing a lot of variants. This is the first one that has matched the UK variant,” McCullers said.

“What I don’t know is if it has some additional variations. It’s likely that all the UK variants out there are also starting to mutate and change a little,” he said.

Confirmation from a public health lab in Nashville or from the Centers for Disease Control will take at least 24 hours.

Shelby County Health Department was alerted late Monday night. The specimen was sent to Nashville early Tuesday.

The strain is about three times more contagious, but not proven to be more fatal, according to David Sweat, Health Department deputy director.

For weeks now, labs here that use the Thermo Fisher processing equipment have been able to quickly identify samples that mimic the UK strain. They are sent to UTHSC along with the random samples from testing sites across the city.

The samples represent about 4% of total testing right now, a tiny sliver, which means variant strains sweeping the world could already be in the region.

One of the clues is a drop-off of the S protein, which the UK variant has. Several of the large labs in town, including AEL, Compass and Poplar Healthcare, are prioritizing work flow so Memphis samples are run on the Thermo Fisher.

But there isn’t any way to tell if the labs are seeing upticks in the missing S protein because there isn’t a baseline in which to compare the numbers.

“No one was doing this before,” said Jim Sweeney, head of Poplar Healthcare. “We don’t know how many S drop-offs there were six months ago.

“There could be variants from the other proteins too. One way to quickly help identify them is if you see an S drop-off, ‘I may want to sequence that,’” he said.

Poplar Healthcare is setting up equipment to sequence suspicious samples itself, preparing to do 150-180 a week.

All the labs in town are aware of the importance of doing sequencing too, he said.

“UT has a very good lab,” he said. “Colleen Jonsson’s lab does outstanding work. They are a first-class organization.”

The United States lags other developed nations in virus sequencing. In early January, it ranked No. 43 in the world.

Having sequenced specimens for comparison, including sequences from early in the pandemic, helps researchers know if and where the virus is mutating.

“That’s how we were able to determine internationally that reinfections seem to occur,” Dr. Stephen Threlkeld said in an interview in January. “People had to have sequenced the earlier viruses and be able to compare those to the new virus from infection three months later.”

The Health Department and COVID-19 joint task force have developed plans to respond to possible variant cases, including how it will manage contact tracing. 

The Health Department’s most experienced investigators will be assigned to these cases, if they materialize.

“It’s something we definitely need to send to a team for special handling,” Sweat said.

Other cases have been suspicious here. When the DNA strands were sequenced they turned out to be normal, he said.

The first line of defense against the virus and any variants is the masking, distancing and hand-washing citizens here have been doing since March.

“If enough people are vaccinated, then yes, that becomes a primary prevention,” Sweat said.

“But we are only right now a little above 7% of our goal. We need to vaccinate 656,600 people in Shelby County in order to reach the target goal of 70% of the population.”

That means the primary protections are the safeguards, which include staying home from work when sick. People placed under isolation orders need to adhere to them.

“Stay home for the period of time that you’re infectious and avoid contact with other people, even in your own home,” Sweat said. “If you’ve been identified as a contact of somebody who’s in quarantine, go ahead and quarantine for the period of time that you are directed to do. All of these things together can help us whether the virus that we’re dealing with is the strain we’ve been fighting since last or is a newly emergent strain.”


coronavirus Jon McCullers Scott Strome
Jane Roberts

Jane Roberts

Longtime journalist Jane Roberts is a Minnesotan by birth and a Memphian by choice. She's lived and reported in the city more than two decades. She covers business news and features for The Daily Memphian.


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