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Omicron Mutations: What to Know About the Latest Subvariants

BA.2, BA.2.12.1 and other circulating strains all fall under omicron’s umbrella

illustration of a gloved hand holding a test tube of COVID-19
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We’ve seen a steep decline in the number of COVID-19 cases since winter’s record-breaking surge, but the variant responsible for that swell hasn’t made as swift a retreat. In fact, omicron has given rise to a number of subvariants — think of them like branches in the omicron family tree — that continue to drive new infections in the U.S. and other areas of the world.

BA.2, sometimes called “stealth omicron,” is responsible for about 62 percent of new COVID-19 cases in the U.S. And its descendant, BA.2.12.1, is behind nearly 37 percent of new infections, the latest data from the Centers for Disease Control and Prevention (CDC) shows. Global health officials are also keeping an eye on omicron subvariants BA.4 and BA.5, which have been reported in South Africa and some countries in Europe.

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Omicron’s subvariants appear more contagious  

It’s not unusual for coronavirus variants to produce sublineages, says Egon Ozer, M.D., an assistant professor at Northwestern’s Feinberg School of Medicine and director of the Center for Pathogen Genomics and Microbial Evolution at the Havey Institute for Global Health. In fact, the delta variant, which dominated the summer and fall of 2021, had several.

The difference is, “they tended to kind of coexist,” Ozer says about the subvariants that made up delta’s family tree. “They didn’t seem like they were necessarily competing with each other.”

With omicron, however, the latest offshoots seem to have a leg up on their parent variant when it comes to transmissibility. The BA.2 subvariant edged out the original omicron strain (also known as BA.1) for the dominant spot after the winter surge, essentially rendering it obsolete. And BA.2.12.1 “might have a transmission advantage of about 25 percent over the BA.2 subvariant,” CDC Director Rochelle Walensky said in an April 26 news briefing.

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Similarly, officials at the World Health Organization (WHO) said in a recent report that subvariants BA.4 and BA.5 — which are driving up COVID-19 cases in South Africa after a long lull — appear to be more contagious than BA.2, though some experts suggest that waning immunity from the early omicron wave could be contributing to the increase in new infections.

It’s possible this pattern — where each wave or bump is caused by a variant more contagious than the last — could peter out, but experts aren’t certain. “At some point, I think the virus is going to reach a tipping point where it’s just not going to be able to declare any greater improvement in transmissibility,” David Montefiori, M.D., a professor and director of the Laboratory for AIDS Vaccine Research and Development at Duke University Medical Center, said in a recent news briefing. “When we’ll reach that point is really difficult to say, but we are seeing the virus continuing to be able to evolve and become more contagious.”

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Vaccines, boosters still working against new variants

The good news: The new variants “do not appear to be any more pathogenic,” Montefiori says, meaning they are not causing people to become more severely ill. “And as far as we can tell, the vaccines are still very effective against all of the variants,” he added.

Omicron is better able to sneak around some of the protections afforded by the vaccines, which is why we saw a spike in infections during the winter surge, including breakthrough infections among vaccinated people. But the shots are still highly effective at preventing some of the worst outcomes of COVID-19. At the height of the omicron wave, unvaccinated adults age 65 and older were six times more likely to be hospitalized with COVID-19 than their vaccinated peers, CDC data shows.

That said, “it’s very important” to get boosted against the omicron subvariants, says Montefiori. Research shows that two doses of the Pfizer or Moderna vaccines provided “limited protection” against symptomatic disease caused by an omicron infection. The booster, however, significantly increased that protection. Adults 50 and older are also eligible for a second booster shot.

And while a handful of monoclonal antibodies that helped treat COVID-19 caused by the delta variant were rendered powerless against omicron and BA.2, the latest treatment, an antiviral pill from Pfizer called Paxlovid, still works at lessening the severity of illness, experts say. So do coronavirus tests.

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“Fortunately, the tests aren’t affected very much by the variants. They are based on multiple portions of the virus,” Montefiori says. “So far the tests, for the most part, are still very effective with all these variants and subvariants of the virus.”

Fate of future variants is unknown

It could be the case that the omicron lineage continues to dominate and that future concerning variants fall under its umbrella, but there’s no guarantee.

“Every three to four or five months, there’s been a new variant that has emerged that is not the descendant of the currently circulating variant,” Ozer says. “Omicron did not come from delta, and delta did not come from alpha or gamma. … And so it remains to be seen whether there are other variants that are going to emerge and outcompete this one. I think time will tell.”

Both Pfizer and Moderna are working on updated versions of their vaccines in hopes of better targeting omicron and any other future variants. These shots, currently being tested in clinical trials, could be available as soon as fall.

But experts say that if you haven’t had your first booster, don’t wait. Less than half of Americans eligible for a booster dose have received one, federal data shows.

“I can’t emphasize enough how important it really is to get boosted for omicron,” Montefiori says. “There’s no question about the need for the boost now to protect against serious illness and death in the case of an omicron infection.” 

Rachel Nania writes about health care and health policy for AARP. Previously she was a reporter and editor for WTOP Radio in Washington, D.C. A recipient of a Gracie Award and a regional Edward R. Murrow Award, she also participated in a dementia fellowship with the National Press Foundation.​

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