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A highly suspicious sample of COVID-19 found in Shelby County is the UK variant strain B.1.1.7, according to officials at the University of Tennessee’s Health Science Center.
The sample was sequenced in the regional biocontainment lab on campus and sent to Nashville for confirmation.
“The hamburger is already done; they just put a little ketchup on it, ”said Dr. Scott Strome, executive dean of the University of Tennessee School of Medicine. “We have a British variant.”
The sample has the genetic markers that match the variant. It was detected in one of the local laboratories.
For weeks, Colleen Jonsson, head of the biological containment lab, sequenced more than 100 virus samples from test sites across the city, looking for variants, especially the four most contagious strains, including the British strain.
By March, Dr. Jon McCullers expects considerable levels of the variant to be available.
“We see a lot of variations. This is the first that matches the British variant, ”said McCullers.
“What I don’t know is if it has additional variations. It is likely that all of the UK variants will also start mutating and changing a bit, ”he said.
Confirmation from a public health lab in Nashville or the Centers for Disease Control will take at least 24 hours.
The Shelby County Health Department was alerted late Monday evening. The specimen was sent to Nashville early Tuesday.
The strain is about three times more contagious, but has not been shown to be more deadly, according to David Sweat, deputy director of the health department.
For weeks, laboratories using Thermo Fisher processing equipment have been able to quickly identify samples that mimic the British strain. They are sent to UTHCS along with random samples from all city test sites.
They make up about 4% of the total testing right now, a tiny sliver, meaning that globally sweeping variants might already be in the region.
One of the clues is a drop in the S protein, which the British variant has. Several of the city’s major labs, including AEL, Compass, and Poplar Healthcare, prioritize workflow to get Memphis samples analyzed on the Thermo Fisher.
But there’s no way to know if labs are seeing an increase in missing protein S because there is no baseline against which to compare the numbers.
“No one did this before,” said Jim Sweeney, director of Poplar Healthcare. “We don’t know how many S deposits there were six months ago.
“There could also be variants of the other proteins. One way to quickly help identify them is if you see an S drop, “I might want to sequence that,” ”he says.
Poplar Healthcare is setting up equipment to sequence suspicious samples on its own, preparing to put in 150-180 points per week.
All of the city’s labs are also aware of the importance of doing sequencing, he said.
“UT has a very good lab,” he says. “Colleen Jonsson’s lab is doing an amazing job. It is a first-rate organization. “
The United States lags behind other developed countries in virus sequencing. At the beginning of January, he was ranked 43rd in the world.
Having sequenced samples for comparison, including sequences from the start of the pandemic, helps researchers know if and where the virus is mutating.
“This is how we were able to determine internationally that re-infections appear to be occurring,” Dr Stephen Threlkeld said in an interview in January. “People had to have sequenced previous viruses and be able to compare them to the new infection virus three months later.”
The Department of Health and the COVID-19 Joint Task Force have made plans to respond to possible cases of variants, including how it will handle contact tracing.
The most experienced investigators in the Department of Health will be assigned to these cases, if they materialize.
“This is something that we absolutely have to send to a team for special treatment,” Sweat said.
Other cases have been suspected here. When the DNA strands were sequenced, they were found to be normal, he said.
The first line of defense against the virus and its variants is the masking, distancing and hand washing that citizens have been doing here since March.
“If enough people are vaccinated, then yes, it becomes primary prevention,” Sweat said.
“But we are currently only exceeding a little over 7% of our target. We need to vaccinate 656,600 people in Shelby County to meet the target of 70% of the population. “
This means that the main protections are guarantees, which include not working at home in the event of illness. People placed under isolation order must adhere to it.
“Stay home during the period of time that you are contagious and avoid contact with other people, even in your own home,” Sweat said. “If you have been identified as a contact of someone who is in quarantine, go ahead and quarantine for the period of time that you are asked to do. All of these things together can help us know whether the virus we are dealing with is the strain we’ve been battling for the last time or is a newly emerging strain.
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