Local scientists, labs rushing to sequence UK variant

By , Daily Memphian Published: January 11, 2021 4:00 AM CT

Scientists in Memphis are in a race against time to build a broader base for identifying coronavirus mutations, starting with U.K. strain B117, which has locked down the United Kingdom.

As of Friday, Jan. 8, 50 cases had been reported in the United States, including a possible case in Chattanooga.

Identifying the mutation requires “fingerprinting” or sequencing its DNA, a laborious task the University of Tennessee Health Science Center is performing now in its regional biocontainment lab run by Colleen Jonsson.

“We don’t know if it’s here or not at the present,” said Dr. Manoj Jain, an infectious disease physician who helped the City of Memphis build its coronavirus testing capacity and now is leading the charge to recognize mutations that could quickly overwhelm health care systems.

“This mutation has a reproduction rate 0.5 greater than what we already have,” Jain said. “If we were having an epidemic with the mutant strain, it would be 1.57. It would create tremendous pressure in terms of cases. A huge number of cases would occur.”

At Shelby County’s current reproduction rate of 1.07, 10 cases turn into 107 and multiply from there. At.1.57, the first rung on the ladder would be 157 new cases, which is a significant difference.

It’s not that the mutation is more virulent, but as the number of cases ramps up, so do fatalities, which is what Shelby County and the rest of the nation are seeing now.

In the last two weeks, the local death toll from COVID-19 has risen more than 20%, from 841 to 1,024 on Jan. 10.

The coronavirus is made up of a series of proteins, including the S protein. One of the major characteristics of the U.K. mutation is that the S sequence is dropped or missing.


COVID surge taxing contact tracing efforts of Health Dept.


The Thermo Fisher platform, which several Memphis labs use to process samples, identifies samples missing the S sequence.

To get a read on whether the mutation may already be in the community, local labs are processing specimens from Shelby County on those platforms and watching carefully.

“We can quickly determine, did the S protein drop off or not,” said Jim Sweeney, chief executive of Poplar Healthcare. “If it did, well, guess what? That is a case we may want to do a complete sequencing of and look at the coding of the DNA to see if it matches the one in the U.K. or South Africa.”

Those samples now are being sent to Colleen Jonsson’s lab for sequencing. Researchers from St. Jude Children’s Research Hospital are assisting.

“We are looking at the S drop strain; we are also looking at randomly choosing 100 samples per week and testing them to see what other kinds of strains are in the region,” Jain said.

The sequencing collaboration also includes the Shelby County Health Department, City of Memphis, American Esoteric Laboratories and Compass Labs.

“UT has been gracious to share the protocol because we are in this together,” Sweeney said. “With the help of Illumina, a sequencing company, we are procuring the necessary reagents and materials to do the sequencing ourselves.”

The key is capacity to detect, Jain says.

“We want to begin to sequence and look at sequencing in addition to the standard testing because it will tell us if there is a variant strain in our community,” he said. “That is what is going to make the difference in stopping this mutant strain from turning into community transmission.”


Vaccine and virus offer high hopes and worst fears at same time


The U.S. lags other developed nations in the sequencing of this virus, which makes it more vulnerable now.

The very simple reality is we are likely about to face a new virus that is going to have a significantly higher ability to spread among us, and we may be facing an opponent that will be much less forgiving of our unwillingness to follow the letter of the infection-control principles that we really haven’t followed so well up to now.

Dr. Stephen Threlkeld
Director of the infectious disease center
at Baptist Memorial Hospital-Memphis

“The last I saw, we were 43rd in the world in sequencing coronavirus variants,” said Dr. Stephen Threlkeld, director of the infectious disease center at Baptist Memorial Hospital-Memphis. “And for a country at the top in biotechnology, that is probably a little lower than we would like at this point.”

Most viral mutations have little or no impact on how they interact with the human immune system. Some mutations weaken the virus or make it impossible to replicate. Some, Threlkeld said, including the U.K. and likely the South Africa variants, seem to fortify them and make them more contagious.

More specimens for comparison, including sequences from early in the pandemic, he said, would help researchers make comparisons and know where changes are occurring.

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

So far, labs say the dropped S strain is somewhat rare, that the rate of transmission and mortality indicate one strain is still dominant.

Knowing that the mutation is in Tennessee, Kentucky and Montana, Threlkeld says, makes little difference on the surface but could be profound if it leads to people being more careful.

“The very simple reality is we are likely about to face a new virus that is going to have a significantly higher ability to spread among us,” Threlkeld said, “and we may be facing an opponent that will be much less forgiving of our unwillingness to follow the letter of the infection-control principles that we really haven’t followed so well up to now.”

For Jain, more sequencing would help identify the mutation and other mutations so cases could be quickly reported, the people put in isolation, and their contacts in quarantine.

“That is what is going to make all the difference in stopping this mutant strain from turning into community transmission,” Jain said.

“The longer we can delay the mutant virus from actively spreading in our community, the better off we will be in terms of managing the epidemic, and it also gives us a chance to vaccinate more people and ultimately prevent it from taking over,” he said.

Preliminary but unpublished and non-peer reviewed reports Jan. 8 showed the Pfizer vaccine worked effectively against one of the key mutations in the U.K. variant in terms of the antibody’s ability to neutralize it.

“It’s a first step,” Threlkeld said, “but it certainly is very encouraging too.”

Topics

Dr. Stephen Threlkeld UTHSC UK variant Jim Sweeney Dr. Manoj Jain Dr. Colleen Jonsson coronavirus pandemic
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 healthcare and higher education for The Daily Memphian.


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