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This illustration, created at the Centers for Disease Control and Prevention, reveals ultrastructural morphology exhibited by coronaviruses. (Provided by the CDC)

The omicron COVID-19 variant has been detected in a Colorado woman who recently traveled to countries in southern Africa, Gov. Jared Polis and state public health officials announced Thursday.

The woman lived in Arapahoe County and returned to Colorado late last week.

“She is experiencing minor symptoms and is isolated and recuperating at home,” the Colorado Department of Public Health and Environment said in a news release. “She had been fully vaccinated and was eligible for the booster vaccine but had not received it yet.”

Colorado is the third U.S. state to detect an omicron case. The first case was detected in California and announced Wednesday. A second case was detected in Minnesota and also announced Thursday.

“At this point,” Polis said during a news conference at the governor’s mansion in downtown Denver, “I’m not terribly alarmed.”

The case was detected through investigation by Tri-County Health Department and CDPHE. After the variant began to emerge around the world, the departments searched through the most recent positive test results here to find people who had reported a recent travel history. That flagged the Arapahoe County woman’s case for full genetic sequencing, which confirmed the infection was caused by the omicron variant.

Dr. Rachel Herlihy, the state epidemiologist, said the woman had recently traveled as a tourist to multiple countries in southern Africa, though she didn’t specify which countries the woman visited. Herlihy said the woman traveled through Denver International Airport. She tested positive a day after returning home when she began experiencing symptoms.

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Herlihy said the woman wore a mask during travel.

Public health officials have ordered the woman to isolate. Her close contacts have tested negative for the disease, according to CDPHE. State officials say they are working with the Centers for Disease Control and Prevention to identify anyone who may have been exposed to the woman during air travel.

Omicron was first identified in South Africa last week and there’s still a lot experts don’t know about the new variant, including how easily it spreads between people or the severity of symptoms, Herlihy said during a news conference earlier this week.

It’s possible, she said, that the variant could be more transmissible or may mutate in a way that makes it more adept at evading the body’s immune system, potentially causing reinfection.

“We have no reason to believe masks would be less effective for the omicron variant,” Herlihy said.

It may be several weeks before epidemiologists get a better understanding of the risks of the variant. 

“Like everybody else,” Polis said, ” we’re looking forward to what information scientists can put out about the omicron variant and its impact on virulence, on how contagious it is and on vaccine efficacy.”

Polis said in a Facebook post that omicron’s discovery in Colorado does not mean it’s time to panic, but that it’s a “time for caution.” Officials were anticipating the variant to be detected in Colorado.

“This was expected news,” Polis said. “We knew it wasn’t a matter of if, it was a matter of when it was identified in Colorado.”

How Colorado is monitoring for omicron

Colorado has two large-scale efforts underway to look for new variants of the coronavirus.

One involves testing wastewater for the presence of the virus. Polis said the state has not found the omicron variant during that surveillance, so far.

The second involves conducting genetic sequencing on a sample of positive tests — the state is currently sequencing about 15% of positive cases, one of the highest rates in the country.

Colorado’s systems, as well as a quirk in omicron’s genetic code, made it likely the state would quickly find the variant once it showed up here.

A basic PCR test — Colorado’s state lab and most of the labs running community testing sites use one called the Thermo Fisher TaqPath Combo test — looks for fragments of the virus’ genetic code. In the case of the TaqPath test, it targets three genetic sites on the virus, labeled orf1a/b, N, and S.

The S site codes for the virus’s spike protein. Omicron’s spike protein is massively mutated from what the test has been designed to detect, though. As Thermo Fisher Scientific Inc. announced Tuesday, when its test scans an omicron sample, it doesn’t detect the S site but picks up on the other two.

This leads to what is called an “S-drop profile” in the test result, which is a red flag to public health workers that the case involves a variant. When a lab gets a result with an S-drop profile in Colorado, it immediately sends it in for full genetic sequencing, which will be able to confirm the variant, Emily Travanty, the director of the state lab, said during a news conference on Tuesday.

The alpha variant — also known as B.1.1.7., the one that was first identified in the United Kingdom — had the same quirk. Colorado was the first state in the country to spot that variant.

“We have very good screening and detection in Colorado,” Polis said Thursday.

Colorado’s COVID situation has been improving

The discovery of the omicron variant in Colorado comes as COVID hospitalizations and cases in the state are trending downward after a prolonged surge.

“We’re less worried about exceeding our hospital capacity than we were two weeks ago,” said Polis. “But when this virus throws spitball after screwball, who knows where we will be two weeks from now, especially after the holiday gatherings.”

The number of people hospitalized because of COVID-19 in Colorado has been steadily decreasing in recent days. As of Thursday, there were 1,400 people hospitalized with the disease, down from more than 1,500 last week.

The number of new cases have been going down too, though Herlihy warned that the Thanksgiving holiday likely affected those statistics.

“We are seeing a pretty dramatic decrease in cases right now,” Herlihy said. “But we think that at least part of that dramatic increase in cases is associated with the Thanksgiving holiday. We know that over the Thanksgiving holiday, that individuals are less likely to seek testing, there might be fewer testing sites open.”

John Ingold is a co-founder of The Colorado Sun and a reporter currently specializing in health care coverage.

Born and raised in Colorado Springs, John spent 18 years working at The Denver Post. Prior to that, he held internships at the Rocky Ford Daily Gazette, the Colorado Springs Gazette and the Rocky Mountain News, among other publications. He also interned one summer in the public relations office at the Cheyenne Mountain Zoo, where he got to sit on an elephant's knee and get his photo taken.

John was part of The Denver Post's 2013 Pulitzer Prize-winning breaking news team for its coverage of a shooting at an Aurora movie theater, and, in 2015, he was a Pulitzer finalist for a series he wrote on parents whose children suffer from a rare form of epilepsy and the help they hoped to find through Colorado's medical marijuana system.

Email: Twitter: @johningold

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Jesse Paul is a Denver-based political reporter and editor at The Colorado Sun, covering the state legislature, Congress and local politics. He is the author of The Unaffiliated newsletter and also occasionally fills in on breaking news coverage.

A Colorado College graduate, Jesse worked at The Denver Post from June 2014 until July 2018, when he joined The Sun. He was also an intern at The Gazette in Colorado Springs and The News Journal in Wilmington, Delaware, his hometown.

Jesse has won awards for long form feature writing, public service reporting, sustained coverage and deadline news reporting.

Email: Twitter: @jesseapaul