The new 'stealth' omicron variant hasn't yet caught on in the US. Scientists are asking why.

Two years into the pandemic, coronavirus continues to throw curveballs. In some countries the omicron "stealth" subvariant BA.2 is rapidly replacing other variants, while in others it's barely a blip.  

It's possible this is due to some underlying attributes of the mutation. Some scientists suggest, however, it just arrived a little late.

One thing researchers have determined is BA.2 isn’t an offshoot of the original omicron variant, known as BA.1. They both split off from an earlier mutation, probably about a year ago. 

“They’re sister variants,” said Dr. Marcel Curlin, a professor of medicine and infectious diseases at the Oregon Health and Science University in Portland, Oregon. BA.2 has been dubbed "stealth” because it doesn’t stand out in PCR tests like BA.1.

As of this week, Denmark reported the subvariant has overtaken all other variants making up 78% of sequenced cases, according to the Danish Serum Institute.

It's also spreading quickly in the United Kingdom, India and the Philippines. 

But In the United States, just 1.5% of sequenced samples are BA.2.

That's puzzling because the subvariant appears to be better able to spread than the original omicron, said Dr. Jacob Lemieux, an infectious disease expert at Massachusetts General Hospital.

"Why is it taking so long to take off here? Is it not coming or is it just delayed in its arrival? We'll be watching that closely," Lemieux said. 

One theory is that its timing was off.

“BA.1 got supercharged by being introduced right in the run-up to the winter holidays," where it spread readily at holiday gatherings, said William Hanage, a professor of epidemiology at Harvard T.H. Chan School of Public Health.

By arriving in the U.S. later, BA.2 “was late to the party,” missing all those opportunities for transmission. “At that point, you’ve only got one big party on New Year’s Eve to exploit,” he said.

Despite being one and a half times more infectious than the original omicron, BA.2 “didn’t get that free ride,” said Curlin.

The good news is that BA.2 doesn't appear to be more virulent. Preliminary data shows no evidence for increased hospitalization from BA.2 compared to BA.1, Lemieux said.

"It's probably not going to radically reshape the pandemic in the way that the BA.1 did," he said.

The big question is whether BA.2 is different enough that it can cause reinfection. So far no data provides the answer, though several investigations are underway.

“There are some reports out of South Africa suggesting there are increases in cases of BA.2 in areas that previously had a large surge of BA.1. But whether those are reinfections or not is still not clear,” said Andy Pekosz, a virologist and and professor at Johns Hopkins Bloomberg School of Public Health.

“Right now it looks like most of the BA.2 infections are in new individuals who haven’t been infected (with BA.1)," he said.

The two subvariants should be close enough that an infection with one protects an infection with another.

“You’ve still got this screaming-hot antibody response, so the same thing that ended your current infection should prevent you from getting a new one,” said Curlin.

A bright spot is that current vaccines also appear to continue to be protective against symptomatic disease for BA.2, said Lemieux.

But a paper published Wednesday suggested that contrary to previous reports, omicron may not be much less severe than delta and other variants.  

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The piece in the New England Journal of Medicine proposed that omicron isn't intrinsically milder but may only appear so because large numbers of people have built up immunity to the virus, either through infection with previous variants or vaccination. 

"Omicron is not as bad as delta, but it’s not much less bad if you’re unvaccinated or previously infected," said Hanage, one of the piece's co-authors.

As of this week, more than 2,200 people a day are dying of COVID-19, according to CDC. Unvaccinated people are about 94 times more likely to die of the disease than those who are vaccinated and received booster shots.

Nadia Roan, a virologist at Gladstone Institutes in San Francisco, said omicron's appearance of relative mildness is probably a feature of both prior immunity and a slight decrease in virulence.

Studies in animals with no prior immunity have demonstrated that omicron is less virulent, and lab studies show that omicron replicates less well in lung-derived cells. But how much this plays out in the real world is not clear.

“I think the evidence is clear that pre-existing immunity plays a major role in omicron's diminished virulence in the population,” she said.

When Dr. Warner Greene, also a virology expert at the Gladstone Institutes, peers into his “somewhat cloudy crystal ball,” he sees the highly infectious omicron variants moving the world out of a COVID-19 pandemic.

“There's going to be a lot of immunity present,” he said. "Immunity to this variant could look more like our immunity to the seasonal coronaviruses (the common cold), where you can be infected with one of these coronaviruses in the fall and again in the spring."

The big caveat is if a virulent variant emerges that can elude the protection of vaccines.

“Knock on wood, we've never seen such a variant," he said. "But this virus continues to evolve, and we do not know in which direction the next variant will come at us from."

Contributing: Karen Weintraub.