A top scientist at the Utah Department of Health said Wednesday that the omicron variant is now likely responsible for more than 70% of the state’s COVID-19 cases, a jump from an estimate made earlier this week.

Utah cases hit 3,303 Wednesday, the most since the worst of the pandemic in early January and a result of the rapid spread of the omicron variant alongside holiday celebrations, the state health department said.

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The state’s estimated omicron cases are going up, too, even though the U.S. Centers for Disease Control and Prevention reduced a previous projection of the percent of the nation’s COVID-19 cases from omicron for the week of Dec. 18 by nearly 50 points, from 73% to 25%.

The CDC’s latest projection of U.S. omicron cases show they’ve reached just under 59% as of Dec. 25.

Some states, including New York, are seeing record numbers of COVID-19 cases due to the new variant already dominant in Utah.

Why Utah’s omicron estimates are even higher

“Our estimate is based more off of direct observation,” unlike the complex mathematical model used by the CDC, said Kelly Oakeson, the state health department’s chief scientist for next-generation sequencing and bioinformatics.

Oakeson said the Utah agency relies primarily on the results of sequencing samples of positive PCR, or polymerase chain reaction, tests for COVID-19 to determine what variant caused the infection.

Utah is sequencing close to 30% of all the positive PCR test results, some 1,500 samples every other day, he said. The omicron variant, first detected in South Africa in late November, was identified in Utah earlier this month.

“For a variant, it’s hard. The only way to confirm a variant has caused somebody to get sick is by sequencing the virus, the entire genome of the virus,” Oakeson said. “That always lags behind the testing by two weeks or so.”

That’s where modeling comes in, but he said Utah doesn’t need to consider as many complicated factors as the CDC does to come up with an estimate of a variant’s presence for a much more diverse national population.

On Dec. 20, when just seven omicron cases had been identified in Utah, the estimate was that the new variant was behind 30% of the state’s COVID-19 infections. By Monday, when the number of cases had increased to 26, the estimate was raised to 65%.

The actual number of omicron cases, however, may have already surpassed that number.

“We’re probably a little bit higher than that now, based on the data we’re seeing for the past couple of days,” Oakeson said, citing an increase in the number of samples tested where a spike gene isn’t showing up because of mutations in the omicron variant.

He said the percentage of Utah’s COVID-19 cases due to omicron is “probably closer to 70%, 74%, somewhere in there, for the past couple of days.” And that number is only going to go up, Oakeson said, given national and international trends.

Sharp surges have been reported around the world as well as in some states like New York that have record case counts and are seeing overcrowded hospitals, store closures, flight cancellations and other issues as workers are sidelined by the virus.

“We’re going to see those same spikes in cases,” Oakeson said. “It’s just a matter of time.”

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Utah sees dramatic COVID-19 case increase

Wednesday’s dramatic COVID-19 case counts in Utah, up nearly 1,500 from Tuesday, “affect ALL Utah residents,” state health department spokeswoman Charla Haley said in a statement, urging all Utahns to help.

“If you feel sick, stay home, and get tested. If you attend a large indoor gathering, we recommend wearing a mask to protect you and those around you. If you have delayed getting your booster or your first vaccine dose, now is the time to get that shot,” she said.

Han Kim, a professor of public health at Westminster College in Salt Lake City, had predicted Monday that Utah would see an omicron-driven surge in COVID-19 cases as soon as the end of the week.

But even Kim was surprised at the number of new cases reported Wednesday.

The professor said he expected the daily total to reach around 2,000 by Friday. Instead, the number of new cases has blown past the highs seen in early November, when Utah and other mountain west states were the nation’s hot spot for the virus.

“This was always the fear, given how quickly omicron spreads. The doubling time is one to three days,” Kim said, adding that at this point, he “wouldn’t be shocked to see 5,000 by Friday.”

The highest number of coronavirus reported in Utah on a single day was 4,706, on Dec. 30, 2020.

Utahns, Kim said, may want to celebrate New Year’s Eve at home and hold off on other plans for now, given how much more transmissible the new variant is, even compared to the highly contagious delta variant that fueled previous surges.

Many Utahns may already be infected and just not realize it, including those who have gotten vaccinated, he said, because in addition to asymptomatic but still spreadable cases, “there’s a lot of coughing, sniffles and cold-like symptoms that could be omicron.”

Much is still unknown about the new variant, Kim said.

“All indications seem to say omicron is a bit milder. But I’m not flat out ready to say, ‘Hey, it’s mild, don’t worry about it,’” he said, since the sheer numbers of cases likely mean hospitalizations and deaths will be high, especially in the unvaccinated.

Utah’s rolling seven-day average for positive tests, which recently had dipped below 1,000, is now at 1,571 per day. The rolling seven-day average for percent positivity of tests is 12% when all results are included, and 8.2% when multiple tests by an individual are excluded.

Tests for the virus continue to be in demand, with 15,338 people tested in Utah since Tuesday, and a total of 27,774 tests conducted, although home testing results are not reported to the state.

Another 12,077 Utahns have been vaccinated in the past day, but less than 59% of all Utahns are considered fully vaccinated, meaning it’s been two weeks or more since their final initial dose. Only about a third of the fully vaccinated have gotten a booster shot.

Also Wednesday, 442 people were reported hospitalized with the virus and there have been seven additional deaths from COVID-19. The latest deaths, which bring the state’s death toll from the virus to 3,781, are:

  • A Utah County woman, between 65 and 84, hospitalized at time of death.
  • A Salt Lake County man, between 65 and 84, hospitalized at time of death.
  • A Tooele County man, between 45 and 64, unknown if hospitalized at time of death.
  • A Tooele County woman, between 65 and 84, hospitalized at time of death.
  • A Salt Lake County woman, between 65 and 84, long-term care facility resident.
  • A Utah County woman, between 65 and 84, unknown if hospitalized at time of death.
  • A Weber County man, older than 85, hospitalized at time of death.