Here's why the new COVID-19 strain being monitored by the CDC stands out

BreAnne Anderson, a registered nurse, administers a COVID-19 test at a Nomi Health test site at Centennial Park in West Valley City on Friday. A new version of the  omicron variant that may be the best yet at evading immunity from vaccinations or previous infections has been spreading in Utah for at least two months.

BreAnne Anderson, a registered nurse, administers a COVID-19 test at a Nomi Health test site at Centennial Park in West Valley City on Friday. A new version of the omicron variant that may be the best yet at evading immunity from vaccinations or previous infections has been spreading in Utah for at least two months. (Laura Seitz, Deseret News)



Estimated read time: 4-5 minutes

SALT LAKE CITY — A new version of the COVID-19 omicron variant that may be the best yet at evading immunity from vaccinations or previous infections has been spreading in Utah for at least two months.

As of Friday, 75 cases of the omicron subvariant labeled BA.4.6 have been identified in Utah by the state lab's genome sequencing of some 3,000 positive COVID-19 test samples weekly, according to Kelly Oakeson, the Utah Department of Health and Human Services chief scientist for next generation sequencing and bioinformatics.

The subvariant was first detected in Utah on June 7, Oakeson said, and is now estimated by the Centers for Disease Control and Prevention to make up just over 4% of the coronavirus circulating throughout the United States as of the end of July but only slightly more than 2% in the region that includes Utah.

The CDC is now listing BA.4.6 separately on its weekly chart monitoring variant proportions. Dr. Cyrus Shahpar, the White House COVID-19 data director, tweeted earlier this week that the subvariant "has been circulating for several weeks."

Cases of BA.4.6 — actually a subvariant of another COVID-19 subvariant, BA.4, that spread widely overseas but not in the U.S. — are climbing slowly but steadily, especially recently even as another subvariant, BA.5, remains the dominant strain in Utah and the rest of the country.

"Definitely, we've seen more of them in the past week or so," Oakeson said, adding BA.4.6 cases have been "growing faster, sooner" since around mid-July. He said he expects that to continue, noting cases of the subvariant have already hit nearly 11% in the region made up of Iowa, Missouri, Nebraska and Kansas.

What's worrying about BA.4.6 is a spike protein mutation seen in the original omicron variant that suggests it may be better equipped to infect people who've been vaccinated and boosted against COVID-19 as well as those who've had an earlier version of the virus, Oakeson said.

Omicron, of course, fueled last winter's COVID-19 surge thanks to being much more easily spread than previous versions of the virus. But the mutation in the latest strain hasn't shown up in recent omicron subvariants, including the even more transmissible BA.5 subvariant.

"We know, based on previous variants, that this mutation, in this spot of the spike protein, does help it evade the immune response," Oakeson said, but there needs to be more data collected before it's clear what can be expected from BA.4.6.

So far, he said, the subvariant is surpassing BA.4 but has not yet shown it can overtake BA.5, which still accounts for around 90% of positive PCR or polymerase chain reaction tests for COVID-19 that are sequenced in Utah. The 3,000 or so samples sequenced weekly represent slightly less than a quarter of all PCR test results.

"The numbers are still early," Oakeson said. "We're not really sure what that's going to do as it gets bigger and bigger and bigger. Will it eventually stall out like BA.4 did, and stay kind of a small proportion? Or will it start chewing into a portion of BA.5? We don't know yet."

That doesn't mean it's safe to ignore BA.4.6.

"I think people should be paying attention to it, for sure," the chief scientist said. "Knowing what's out there, what's circulating, knowing that even if you're vaccinated you can still get sick and spread that sickness, I think people should be aware of that."

Besides staying up to date on vaccinations and booster shots to protect against severe illness, Oakeson said people should also wear masks in crowded indoor spaces, keep social distancing, and be ready for the possibility of a new wave of infections once school starts.

"It's not one of these things that's just a common cold that doesn't affect us. We're not going to get it once and be done with it. It's going to keep reinfecting us, and it can cause long-term health effects," he said. "We know how to protect ourselves."

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Lisa Riley Roche

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