'Stealth Omicron' Subvariant Detected Across California

LOS ANGELES, CA — The new subvariant of the omicron coronavirus variant, known as BA.2, was detected in California and was expected to spread quickly.

The new subvariant was dubbed "stealth omicron" because its particular genetic traits make it somewhat harder to detect, and evidence suggested it will spread even more quickly than its infamous parent.

California health officials had confirmed a total of 14 BA.2 cases spread out across the state as of Wednesday. BA.2 cases were identified in Los Angeles, Santa Clara, San Diego, Orange and Tulare counties.

The new subvariant was not considered a variant of concern, according to the World Health Organization. In countries such as Denmark, where it quickly became the dominant variant, health officials have not seen an increase in COVID-19 hospitalizations or deaths.

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"New variants will continue to evolve as long as there are large pockets of unvaccinated people," a California Department of Public Health spokesperson told Patch. "Strengthening our protection against COVID-19 through vaccination and boosting is more important than ever."

Among the many questions yet to be answered is how vaccines and natural immunity from prior omicron infection hold up against BA.2

Roughly one in five Californians has been infected with the coronavirus. More than 20 percent of the state's more than 8 million recorded cases have occurred since the start of January, an unprecedented surge fueled by omicron.

California is averaging an 18.7 percent testing positivity rate and roughly 88,000 new cases confirmed each day. Though the state recorded some of the highest daily death tolls of the pandemic this week, omicron has proven to be far less deadly than variants such as delta.

(California Department Of Public Health)
(California Department Of Public Health)

As BA.2 spreads, scientists and health officials around the world were keeping their eyes on the descendant of the omicron variant, which has been found in at least 40 countries, including the United States.

Where Has It Spread?

Since mid-November, more than three dozen countries have uploaded nearly 15,000 genetic sequences of BA.2 to GISAID, a global platform for sharing coronavirus data. As of Tuesday morning, 96 of those sequenced cases came from the U.S.

“Thus far, we haven’t seen it start to gain ground” in the U.S., said Dr. Wesley Long, a pathologist at Houston Methodist in Texas, which identified three cases of BA.2.

The mutant appears much more common in Asia and Europe.

What’s Known About This Version Of The Virus?

BA.2 has lots of mutations. About 20 of them in the spike protein that studs the outside of the virus are shared with the original omicron. But it also has additional genetic changes not seen in the initial version.

It's unclear how significant those mutations are, especially in a population that has encountered the original omicron, said Dr. Jeremy Luban, a virologist at the University of Massachusetts Medical School.

For now, the original version, known as BA.1, and BA.2 are considered subsets of omicron. But global health leaders could give BA.2 its own Greek letter name if it is deemed a globally significant “variant of concern.”

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The quick spread of BA.2 in some places raised concerns it could take off.

“We have some indications that it just may be as contagious or perhaps slightly more contagious than [original] omicron since it’s able to compete with it in some areas,” Long said. “But we don’t necessarily know why that is.”

An initial analysis by scientists in Denmark showed no differences in hospitalizations for BA.2 compared with the original omicron. Scientists there were still looking into the version's infectiousness and how well current vaccines work against it. It's also unclear how well treatments will work against it.

Doctors also don’t yet know for sure if someone who’s already had COVID-19 caused by omicron can be sickened again by BA.2. But they’re hopeful that a prior omicron infection might lessen the severity of disease if someone later contracts BA.2.

The two versions of omicron have enough in common that it’s possible that infection with the original mutant "will give you cross-protection against BA.2,” said Dr. Daniel Kuritzkes, an infectious diseases expert at Brigham and Women’s Hospital.

Scientists will be conducting tests to see if antibodies from an infection with the original omicron "are able to neutralize BA.2 in the laboratory and then extrapolate from there,” he said.

How Concerned Are Health Agencies?

The World Health Organization classified omicron overall as a variant of concern, its most serious designation of a coronavirus mutant. But the agency didn’t single out BA.2 with a designation of its own. Given its rise in some countries, however, the agency said investigations of BA.2 “should be prioritized."

It's too soon to say if BA.2 will become a dominant coronavirus variant, Centers for Disease Control and Prevention spokeswoman Kristen Nordlund told The Washington Post.

"Although the BA.2 lineage has recently increased in proportion in some countries, it remains a very low proportion of circulating viruses in the United States and globally," she said. "Currently, there are insufficient data to determine whether the BA.2 lineage is more transmissible or has a fitness advantage over the BA.1 lineage. CDC continues to monitor variants that are circulating both domestically and internationally."

Why Is It Harder To Detect?

The original version of omicron had specific genetic features that allowed health officials to rapidly differentiate it from delta using a certain PCR test because of what’s known as “S gene target failure.”

BA.2 doesn't have this same genetic quirk. So on the test, Long said, BA.2 looks like delta.

“It's not that the test doesn't detect it; it's just that it doesn't look like omicron,” he said. "Don’t get the impression that ‘stealth omicron’ means we can’t detect it. All of our PCR tests can still detect it.”

What Should You Do To Protect Yourself?

Doctors advised the same precautions they have all along: Get vaccinated and follow public health guidance about wearing masks, avoiding crowds and staying home when you’re sick.

“The vaccines are still providing good defense against severe disease, hospitalization and death,” Long said. “Even if you’ve had COVID 19 before — you’ve had a natural infection — the protection from the vaccine is still stronger, longer lasting and actually ... does well for people who’ve been previously infected.”

The latest version is another reminder that the pandemic hasn't ended.

“We all wish that it was over," Long said, ”but until we get the world vaccinated, we’re going to be at risk of having new variants emerge.”


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The Associated Press and Patch Staffer Beth Dalbey contributed to this report.

This article originally appeared on the Los Angeles Patch