Massive holiday COVID testing sets up busy weeks, months in race to sequence cases of omicron variant

Coronavirus

RALEIGH, N.C. (WNCN) — Dr. Dirk Dittmer and his team of researchers are ready for some busy weeks and months.

Dittmer runs a lab at the University of North Carolina that sequences samples of positive COVID-19 tests for variants — including omicron.

Massive testing numbers before the holidays mean lots of samples that must be checked. And state public health leaders’ concerns about the possibility of 10,000 new cases a day at omicron’s peak only underscores the importance of understanding just how much it is spreading.

“We’re prepared to sequence more samples come January, and that will tell us how fast the omicron (variant) spreads in the state,” Dittmer said.

Dittmer is one of the leaders of the state’s CORVASEQ surveillance program, which started over the summer and pins down the specific COVID variant that turns up in positive PCR tests.

The program has hubs at five universities across the state — UNC-Chapel Hill, UNC-Charlotte, Duke, Wake Forest, and East Carolina — and the one at UNC-Charlotte found the first case of the omicron variant earlier this month.

He says his lab sequences “on the order of 100” samples each day but can perform up to 10 times as many.

“If we need to increase that to 1,000 samples a day, because we’re so many universities, we’re able to capture most of these samples,” Dittmer said.

He says only about 10 percent of samples across the U.S. are sequenced.

How does it work? If your nasal swab is found to be positive, part of that sample may be sent to a sequencing lab where researchers look “at the entire genetic information of the virus” — about 29,000 letters worth, he said.

“And based on the entirety of that information, we can tell you whether this virus is delta, or is omicron, or is something entirely different,” he said.

The sequencing data is reported to the GISAID database, a system of sharing information about the genomic information of flu viruses that does not collect personal information, he said.

The state Department of Health and Human Services receives more detailed demographic information so that the agency “has the ability to look more in detail whether there are hotspots of infection with omicron or whether there is an unusual correlation with, for example, immunization status,” Dittmer said.

NCDHHS issues a weekly breakdown of variants found in the state, and the most recent report released last week was the first to include a case of omicron. The publication indicated omicron was spotted during the week of Dec. 11 and made up fewer than 5 percent of all variant cases, with delta continuing to be the dominant strain in the state.

(Source: NCDHHS)

But omicron is known to spread fast.

“The more omicron is circulating in the state of North Carolina, the more people will become infected, and that helps us prepare hospitals for the upcoming surge,” he said.

Omicron almost certainly won’t be the last variant, either. Dittmer says the CORVASEQ program can detect any other strains that emerge — or even other types of viruses.

“The beauty of sequencing, and the big difference to the specific tests that are used at CVS, is that we’re able to detect any variant that is there,” he said. “We can detect any virus that is there if we change the assay and say, ‘We want to know, and we want to know what influenza variants are circulating.’ That’s the beauty of this technology. It gives us a really detailed view on everything that we want to look at.”


CBS 17’s Joedy McCreary has been tracking COVID-19 figures since March 2020, compiling data from federal, state, and local sources to deliver a clear snapshot of what the coronavirus situation looks like now and what it could look like in the future.


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