Here’s what we know about the omicron variant of COVID-19 so far

Omicron is now the dominant variant in the United States

ORLANDO, Fla. – Amid a new surge in COVID-19 cases in Florida and across the country, the big question is how many of these new cases are of the new omicron variant.

The U.S. does not have a robust sequencing program like other countries, where there’s been an explosion of identified omicron cases.

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“Any given person who gets a COVID test in the United States does not know what variant they are testing positive forward,” said Chad Neilsen, director of infection prevention at the University of Florida Health in Jacksonville. “Which means in order to know, the test has to be sent for genomic sequencing, which most hospitals are not going to do.”

The Centers for Disease Control and Prevention said Monday that omicron is now the dominant variant in the U.S., accounting for 73% of new infections.

But since the U.S. doesn’t have that strong sequencing program, there will be a lag in knowing exactly how many omicron cases there are, when they were identified and where.

Here is what we know about the omicron variant of COVID-19 so far.

Omicron: Virus lineage number B.1.1.529

First detected: South Africa in November

Cases currently found in: 89 countries, according to the World Health Organization

In the U.S., cases are currently found in: 45 states, Washington D.C., and Puerto Rico.

In Florida: Two confirmed cases have been discovered in Miami-Dade and Hillsborough counties a couple of weeks ago. Since then, omicron has overtaken delta as the dominant strain in Miami-Dade County.

The county contracts with NOMI Health to conduct testing, vaccination and sequencing. The company found that 76% of 504 COVID-19 samples taken Dec. 14-15 were the omicron variant. That compared to 64% of 378 samples collected Dec. 10-13, and 1.3% of the 373 samples collected Dec. 1-5, county records showed.

No cases have been confirmed in Central Florida yet. However, the presence of omicron has been detected in wastewater samples in Altamonte Springs’ treatment plant and all three Orange County plants. Since it takes time for cases to be genomically sequenced, we could hear about more individual cases in the coming days and weeks.

The knowns and unknowns of an omicron infection

Data from overseas points to omicron being far more transmissible than delta. In the United Kingdom, omicron replaced delta as the dominant strain in a matter of weeks, with new cases up 60% in a week.

Two recently released preprinted studies, one from Hong Kong University and one from the Ragon Institute of Massachusetts General Hospital, show the omicron variant, which has a heavily mutated spike protein, is better than previous variants at latching onto the receptor the virus uses to enter human cells. This allows it to replicate more quickly in cells and explains why the variant is more infectious.

However, studies out of South Africa, where the variant was first detected, point to the omicron variant also having lower cases of severe illness. While there are more people sick, fewer people ended up in the hospital and of those in the hospital, fewer people ended up in the ICU.

It’s not known yet if that because the population is younger, or if patients have some natural immunity from a recent infection of the delta variant of COVID. South Africa also has a lower vaccination rate.

The preprinted study out of Hong Kong University found that while omicron does spread fast and better than delta in human airways, it also was not as good at severely infecting lung tissue, which might explain why the virus is not as severe.

Since all of these studies are early and preprints, the veracity of these studies has not yet been peer reviewed.

Knowing what variant of COVID a patient has doesn’t matter as much once the patient is at the hospital, said Dr. Ed Jimenez with UF Health Shands Hospital in Gainesville. It also didn’t normally matter with previous variants.

Omicron, however, does appear to be resistant to some treatments, which will make a difference in how the variant is treated, and why it may be important to know what variant of COVID you have.

“It becomes important because let’s say you have omicron,” said Jimenez. “You’re not sick enough to go to the hospital but you need something. What we’ve learned from overseas is that Regeneron (a monoclonal antibody treatment) doesn’t work as well. So, they have to give you something different.”

How do the vaccines handle omicron?

So far, the early studies show omicron is good at evading COVID antibodies. This lessens the effectiveness of the current vaccines in stopping infection, although the vaccines were never 100% effective in stopping infection in the first place. They were highly effective in reducing the risk of getting a severe illness or dying from COVID.

However, early data from both Pfizer and Moderna suggest the booster shot does boost antibody levels and has a significant impact against omicron.

Antibody levels naturally drop over time, and a booster revved them back up again, by 25 times for Pfizer’s extra shot and 37 times for Moderna’s.

The vaccine’s mRNA design brings T-cells that can fight the virus while memory cells activate to make stronger antibodies. This helps in preventing more severe illness.

Johnson & Johnson says it is currently testing the vaccine against omicron.

Experts say a prior infection from COVID doesn’t have as much protection against omicron as it did against delta, and anyone who survived COVID-19 should get vaccinated because the combination of natural and vaccination immunity offers stronger protection.

What will that mean for the future?

New projections from the Emerging Pathogens Institute at UF show we may see tens of thousands of new cases a day in Florida before it peaks.

Researchers came up with four models for how omicron could play out between now and February. All four models agree omicron will start slowly in December, spread rapidly in January and peak in February. One scenario shows reported new cases could reach as high as 40,000 a day by February.

However, Dr. Jimenez says to take these projections with a grain of salt.

“I would say take the information we gave you, it should be close enough, but it may not be exactly right,” he said.

He also cautions that, while all the early reports offer a rosier outlook for omicron, the virus may behave differently here.

“In Florida we still have a high number of unvaccinated people, we’re also the third largest state,” he said. “So, the rate (of hospitalization) might be lower, but with so many unvaccinated people that over time we might end up having equal or more ICU patients. So, time will tell on that.”

Neilsen, meanwhile, is hopeful that omicron will lead COVID-19 in the direction of less virulent virus.

“When swine flu hit the US in 2009 it was devastating, but then it sort of petered out because it mutated into something less virulent,” Neilsen said.

“Our hope is that more people get vaccinated, COVID will mutate into a less virulent form,” he added. “And will weaken into something closer to the common cold.”

Information from the Associated Press was used in this report.

About the Author:

Christie joined the ClickOrlando team in November 2021.