Omicron variant spread has health officials preparing for its arrival in Colorado

By: - November 30, 2021 4:47 pm

Lab Technician Carter Tavaglione loads at Janus G3 automated workstation with coronavirus test samples at Advagenix, a molecular diagnostics laboratory, on Aug. 5, 2020, in Rockville, Maryland. (Chip Somodevilla/Getty Images)

The newly-sequenced omicron coronavirus variant hasn’t been discovered in the United States yet, but Colorado scientists are preparing to identify it as soon as it hits the state through lab sample sequencing and wastewater detection. 

“It’s difficult to know when, so at this point we’re using all the tools we have … to make sure we have the detection systems in place to identify it as quickly as possible once it is here,” state epidemiologist Dr. Rachel Herlihy told reporters on Tuesday.


“At the same time, we are working on the epidemiologic side with our epidemiology team to make sure we are standing up procedures for responding: case investigation, contact tracing, enhanced monitoring for individuals that have come from countries where the infection is spreading more readily,” she said.

The omicron variant was first identified by South African scientists last week and has since been labeled as a “variant of concern” by the World Health Organization. The WHO has said that existing vaccines remain effective in preventing severe illness and death from COVID-19, but more research is needed to understand the specific impact omicron could have.

As of Nov. 30 at 3 p.m., no cases of the variant had been identified in the United States, but there are some in Canada and Western Europe. Nearly every case of COVID-19 in Colorado is the delta variant. 

Herlihy said that there is still a lot to learn about the omicron variant, but based on knowledge about other variants, it’s reasonable to predict that omicron will be more transmissible or that the immune response will be less effective against it. 

“It could be several weeks before we have a good clinical picture, an epidemiological picture, of this variant,” she said.  

Colorado’s state lab has updated its clinical sequencing procedures to identify omicron quickly. If a sample collected through diagnostic testing shows a drop in the spike protein profile — one indicator of the omicron variant — it is immediately forwarded on for clinical sequencing. 

It’s likely that the omicron variant will be detected in wastewater before it is found in that whole-genome sequencing of clinical samples.

The state is searching for the omicron variant through wastewater surveillance, as it did with the delta variant. Since August 2020, the Colorado Department of Public Health and Environment has partnered with 21 wastewater utilities to monitor for the coronavirus, analyzing two samples per week from those utilities. 

“This allows us to look for genetic markers indicative of variants within wastewater,” state lab director Emily Travanty explained. “Variants can be detected in wastewater sooner than in clinical samples and the state lab has recently updated our processes and can now detect these markers in wastewater.”

Same public health strategies for omicron

Epidemiologist Rachel Jervis said that nearly half of people with COVID-19 will shed some of that virus in their stool regardless of whether they have symptoms, so wastewater monitoring could detect new variants before clinical testing.

“I’m confident that through both the clinical sequencing as well as this early warning system with the wastewater sequencing, that we are able to see omicron when it does appear in Colorado,” Travanty said.

Herlihy said that when the omicron variant is detected in Colorado, public health strategies will be unchanged — that means further pushes for vaccinations, mask-wearing and social distancing.

“The strategies that we used for alpha are the same strategies that we’re using now for delta and are the same strategies we’ll use for omicron when it arrives in Colorado and the U.S.,” she said. “It’s the same things that we’ve been doing that we’ve thankfully learned how to do now to suppress transmission.”

As of Nov. 30, there were 1,466 confirmed COVID-19 patients in Colorado hospitals. It’s a slight dip from a recent peak of 1,576 on Nov. 23, but health officials warn that it might not yet reflect cases contracted over Thanksgiving.

“We are seeing improvements in the data. It’s certainly reassuring to see that things appear to be trending in the right direction,” Herlihy said. “But it’s always important to keep in mind that following holidays, we do sometimes see an increase in cases that occur following holiday gatherings and changes in interactions and contacts that people have.”


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Sara Wilson
Sara Wilson

Sara Wilson covers state government, Colorado's congressional delegation, energy and other stories for Newsline. She formerly was a reporter for The Pueblo Chieftain, where she covered politics and government in southern Colorado. Wilson earned a master's degree in journalism from Northwestern University, and as a student she reported on Congress and other federal beats in Washington, D.C.