Omicron COVID-19 variant now overwhelmingly dominant in Arizona, sequencing labs say

The omicron variant of the virus that causes COVID-19 is now overwhelmingly dominant in Arizona, a result that some researchers have been expecting and can now confirm with data, according to sequencing labs at Arizona State University and TGen.

As of Saturday, assistant professor Efrem Lim’s lab at the Biodesign Institute at ASU is reporting on their website that 95% of their sequenced cases are the omicron variant. TGen, which analyzes samples from across the state, also updated their online tracker to show that 87% of their COVID-positive samples as of this week are the omicron variant.

"It's remarkable how quickly Omicron is taking over from Delta," Lim said in an email.

It’s a pattern that has been playing out over the past couple of weeks, but now omicron is outcompeting the previously dominant delta strain, said David Engelthaler, director of the pathogen & microbiome division at TGen. “I have no doubt that this will be not just the dominant, but essentially, the variant that we find in all four corners of the state here within the next week or so,” he said.

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The rapid omicron jump in Arizona has been relatively delayed compared with other parts of the country, some of which are already well into omicron-driven surges. “It does seem like it starts on the East Coast and then it comes here later, and Arizona seems to be at the end of the whip, as it were,” said Joshua LaBaer, director of the Biodesign Institute, in a press briefing on Wednesday.

Deepta Bhattacharya, a professor of immunobiology at the University of Arizona, described the sense of shock he and other researchers experienced watching omicron’s rapid takeoff around the world. “To see something that comes along and takes over Delta at that rate … it’s been surreal watching it, to be honest,” he said.

Both ASU and TGen researchers can detect the omicron variant because after they digitize a sample, they can use computer programs to analyze each positive case, comparing long sequences of letters that stand for different molecular compounds. The omicron variant has some standout variations in those sequences of letters that make it clearly distinguishable from other variants like delta.

Because TGen takes longer to process cases than ASU — their lab sequences positive samples statewide rather than more localized samples — TGen’s data is likely to show a slight lag compared with the most up-to-date numbers. Engelthaler said TGen has shifted its strategy to process smaller batches of samples every day, rather than one large batch over the course of a week, to better reflect case numbers in rural areas. He expects their percentage of omicron cases statewide to move well into the 90% range by the weekend.

Evidence suggests that omicron may induce milder forms of illness than other coronavirus strains. That fact gives Engelthaler hope that this surge, even with the highest daily national case numbers doubling counts from last winter, may not be as catastrophic as surges brought on by previous variants. However, some experts are still concerned about how the sheer number of infections will stress hospital systems in the coming weeks.

“Even though (there is) a small decrease in the virulence, it will be largely offset by the large caseload that we're likely to see here,” LaBaer said.

Some doctors are also worried that the volume of cases could have ripple effects across the healthcare system as hospitals reach capacity.

“Last month the Arizona Public Health Association reported that Arizona saw the greatest percent increase in excess deaths during the pandemic in the entirety of the United States. This is likely a symptom of our constantly overburdened healthcare system,” said Elizabeth Jacobs, a professor of epidemiology and biostatistics at the University of Arizona, in a livestream that brought together some health care workers and advocates calling for better public health mitigation strategies.

“The situation has changed, and we must adjust,” said Dr. Ruth Franks Snedecor, a clinical assistant professor of internal medicine at the University of Arizona College of Medicine in Phoenix, on the same livestream. She added that Arizona hospitals are “in extreme crisis and on the verge of collapse.”

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LaBaer hopes for a return to the idea of “flattening the curve” — slowing the positive infection rate enough to keep the healthcare system afloat. “If we can just keep the spread of this thing a little bit more under control so that we don't overwhelm our hospitals … that would be a laudable goal,” LaBaer said.

Doctors and researchers stressed that vaccinations and boosters will be critical to managing the tide of omicron cases.

“Having been vaccinated will certainly protect you to the extent of significantly reducing the likelihood of hospitalization and death, even from omicron,” La Baer said.

Bhattacharya also said a booster significantly reduces the risk of severe disease. “If you haven’t gotten a third dose, or another dose post-(Johnson & Johnson), I think it’s time to do it,” he said.

He also noted that while case numbers are skyrocketing, that doesn’t mean it is futile to try to prevent further spread of the disease. He said that researchers are focused on furthering research on the virus, improving vaccines and treatment options such as antivirals that can make COVID-19 less dangerous.

“There are chances to avoid omicron,” Bhattacharya said. “It’s going to get harder…(but) if you can hold out for a little longer, there will be better pharmaceutical options.”

Republic reporter Stephanie Innes contributed to this article.

Independent coverage of bioscience in Arizona is supported by a grant from the Flinn Foundation.

Melina Walling is a bioscience reporter who covers COVID-19, health, technology, agriculture and the environment. You can contact her via email at mwalling@gannett.com, or on Twitter @MelinaWalling.

This article originally appeared on Arizona Republic: Omicron variant represents nearly all coronavirus cases in Arizona