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The highly transmissible omicron variant is behind this record-setting surge. It now accounts for the wide majority of cases in ÃÛèÖÖ±²¥ and Pima County.

In the last week of December, nearly 85% of all genetically sequenced COVID-19 cases in ÃÛèÖÖ±²¥ were omicron, a variant that’s even more transmissible than the previously dominant delta variant, according to a new chart published by the Translational Genomics Research Institute, or TGen.

The same thing is playing out in Pima County.

Over the past two weeks here, 51 out of 61 genetically sequenced cases were omicron, said Dr. David Engelthaler, director of TGen’s infectious disease research.

He expects omicron to make up 99% of COVID-19 cases in ÃÛèÖÖ±²¥ within a week.

Now that this variant has solidly taken over, scientists will be looking for any sub-variants of omicron, he said. “Are there any that are actually more important that are causing greater outbreaks, or not?�

Genetic sequencing labs in ÃÛèÖÖ±²¥ don’t have the resources to test all COVID-19 cases for omicron, but they typically sequence between 5% to 8% of cases, he said.

As cases surge, labs will sequence an even smaller percentage of cases because they won’t have the capacity to keep up, Engelthaler said.

More people in ÃÛèÖÖ±²¥ tested positive for COVID-19 on Jan. 3 than any other day during the pandemic, according to data from the ÃÛèÖÖ±²¥ Department of Health Services.

On that day, 13,533 people tested positive, surpassing ÃÛèÖÖ±²¥â€™s previous daily record of 12,447 cases in a day, set last year on Jan. 4.

“This is the fastest rate of rise we’ve seen,â€� said Dr. Joshua LaBaer, executive director of ÃÛèÖÖ±²¥ State University’s Biodesign Institute, adding that while the majority of cases are omicron, some delta cases are lingering.

The window of time where both delta and omicron variants circulate will be short-lived, Engelthaler said.

“During that window of time, there’s been a little bit of concern about whether or not treatments would work because some of the monoclonal antibody treatments don’t work for omicron, but they do work for delta,� he said.

“Since we don’t have variant testing as a diagnostic test that a physician can use right there to determine whether or not their patient can receive a monoclonal antibody, they just have to look at the available population data and make a decision.�

Or, Engelthaler added, local health departments or federal health authorities will make a decision about whether or not to stop using particular drugs.

“We’re really moving out of that window now and it’s quickly becoming all omicron. So all patients will need to be treated like they’re omicron patients.�

Pima County is in this window now. Two Federal Emergency Management Agency teams are currently in the county to help distribute subcutaneous shots of Regeneron, a treatment that boosts the body with antibodies.

“Regeneron is not very effective, if effective at all against omicron,� said Dr. Theresa Cullen, the county’s Health Department director. “The federal government has indicated that if the percentage of omicron in your jurisdiction is less than 80%, they still recommend the use of Regeneron.�

About 84% of genetically sequenced COVID-19 cases have been omicron cases in the last two weeks, according to data cited by Engelthaler; however, the county is continuing to use Regeneron.

“FEMA is allowing us to continue; no impact as of now,� said Anthony Gimino, a spokesman for the county Health Department, on Friday.

Cullen added that the county is planning on also using sotrovimab, a treatment that’s expected to remain effective against omicron.

She also said at a news conference on Wednesday that the delta variant is still resulting in people being hospitalized, and Regeneron is effective against that variant.

In the immediate future, omicron will likely keep driving cases to record levels, but that probably won’t be true for hospitalizations, and almost certainly not deaths, said Dr. Joe Gerald, an associate professor with the University of ÃÛèÖÖ±²¥â€™s College of Public Health.

This is because the population is now generally more immune to COVID-19 than during previous surges, due to vaccinations and previous infections, he said, adding that this doesn’t translate to good news for everyone, such as families who will lose loved ones to COVID-19 in the coming weeks.

“I think our health care system workforce is still going to be incredibly strained,� he said. “Everybody’s going to be busy, but the greatest crushing burden I think is going to be in our triage system.�