Lab that detected Colorado’s first omicron case monitoring for new variants

Coronavirus

DENVER (KDVR) — The team at the Colorado Department of Public Health and Environment’s laboratory was the first to sequence and confirm a case of the omicron variant in the state.

“It was a bit of a flashback to when we were the first laboratory in the country to find the alpha variant, the B-117 variant,” lab director Emily Travanty said.

The lab can process as many as 13,000 PCR tests per day when running at full capacity. 

“If COVID is in the sample, it then moves on to the second level of testing, which is our genomic sequencing,” she said.

Sequencing is the process that determines which type of COVID person has. 

“Every time the virus infects someone, it is making copies of itself. When it makes copies of itself, that’s when it can mutate, and so it’s very important for us to be continually sampling the viruses that are out there circulating and looking for what’s new,” Travanty said. 

Right now, the state’s lab sequences every positive COVID test. However, when they began looking for the omicron variant, they began prioritizing tests from COVID-positive patients with a travel history to South Africa.

“Knowing that there was travel associated with this, that contact tracing level epidemiological work that was done by the CDPHE teams and Tri-County teams really allowed us to take the sample and push it to the front of the line, and ensure that it got sequenced as quickly as possible if it did have the variant or not, because it was high risk,” Travanty said. 

On average, once a PCR test yields a positive result, it can take two days to a week to complete the sequencing.

“We can usually do over 200 samples every few days in the laboratory,” Travanty said. 

While the data answers what kind of COVID is present in the community, it can also help answer questions about how it got there and where it may be going next. 

“We do a second layer of this sort of surveillance testing on them to understand how the samples that affect various people are related to each other,” Travanty said. 

The surveillance can also help detect new strains of the virus that have not yet been detected. 

“Any lab that’s doing sequencing could find a new variant,” Travanty said. 

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