Duke researchers finding few original COVID-19 strains in samples


RALEIGH, N.C. (WNCN) – As students and staff returned to Duke University, they agreed to be part of a campus-wide COVID-19 testing program. Those samples are now being used to determine if any of the faster-spreading mutations of the virus are on campus.

Nadrat Chowdhury, PhD environmental engineering student, scans her Covid-19 test at the Levine Science Research Center (LSRC) on Duke’s West Campus. Courtesy: Duke

“There’s certainly an indication that some of these strains spread faster and if we see those strains come into the community, we want to be aware of those,” Duke biology professor Greg Wray.

Scientists find out if a virus is mutating through a process called sequencing. It looks at the DNA of a virus.

Sequencing genes of virus samples is important because it allows scientists to understand how the virus is spreading.

It also helps with vaccines. There may be some variants that are not impacted by our current vaccines.

“That’s the only way we’re going to learn whether vaccines are starting to not work anymore,” said Wray.

Variants out-competed original strain

The path of Covid-19 testing, from random surveillance testing at the Levine Science Research Center (LSRC) on Duke’s West Campus to processing at a central laboratory based in the School of Medicine’s Duke Human Vaccine Institute. Courtesy: Duke

The original Wuhan strain COVID-19 virus has mutated several times over the course of the last year. While it may have started out as the dominant version of the virus, it’s becoming rarer. Out of more than 200 samples, Duke’s sequencing lab only found the original strain in one sample.

“It’s been out-competed,” said Wray.

Wray said the original was essentially wiped out last year with more contagious versions. Along with increased holiday travel, it may be why case counts started to rise over the winter.

The California and New York strains have been among COVID-19 positive samples at Duke.

“Another reason we need to keep track, we can’t assume the U.K. strain is going to stay in U.K. and the California strain is going to stay in California. We know that’s not going to be the case,” said Wray.

The U.K. strain in particular is believed to keep people infectious longer. That means instead of isolating for 10 days, a person may need to really isolate for 16 to avoid infecting others. Wray said it’s important to know which you have so you don’t over or under quarantine.

Less than 1% of samples analyzed in NC

While a COVID-19 test may be able to tell you whether you have the virus, special labs with a separate set of skills are required to look for mutations.

Right now, Duke is processing a few hundred COVID-19 positive samples a week. Overall, North Carolina is sequencing fewer than 0.30 percent of positive samples. Wray said that’s because most of this work is being done in university settings and very little sequencing is state-mandated.

If the state requested their help, Wray said the lab could sequence a few thousand samples a day.

“We’re ready to go if that’s the case,” he said.

That’s because the university has invested in robotics to speed the process.

“Once the samples have been taken out of the collection tube, pretty much everything is automated now,” said Wray.

Wray hoped the CDC and the federal government could work together to determine a better plan to sequence more samples efficiently. Like vaccines and masking, sequencing will continue to be another tool in the fight against COVID-19.

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