In mid-January, when the omicron variant was driving the Philadelphia area’s latest wave of COVID-19, a boxy white device in Frederic Bushman’s lab already had detected a hint to the pandemic’s next chapter:
The region’s first case of a subvariant of omicron, what would eventually be known as BA.2.
That subvariant has now gained a foothold across the United States, accounting for one-third of new cases nationwide, and more than half of cases in New England as of Saturday, the CDC said .
And this new-ish version of omicron has fueled yet another surge in parts of Europe. Yet so far in the United States, the overall number of cases remains low, down sharply from the peak in January.
Whether we’re due for another surge is unclear. Some infectious-disease experts are predicting that the subvariant may have less of an impact here than in Europe — taking the place of the original omicron without driving a big increase in cases.
That’s partly because the United States was hit so hard by the first wave of omicron. Much of the country had cut back on mask-wearing and other precautions by mid-January, and more people got sick as a result. That means they have the benefit of a fairly recent boost to their immune systems, even if it was acquired in a risky manner.
But the coronavirus has behaved in unpredictable ways. If BA.2 does not fuel a big surge here, another variant will at some point, infectious-disease specialists warn. Vaccination remains the key — for all known variants, vaccines are still effective at preventing severe disease.
Here’s what to know about BA.2, with an assist from Bushman, the chair of microbiology at the University of Pennsylvania’s Perelman School of Medicine, and Maciej Boni, an associate professor of biology at Pennsylvania State University.
Where’d they get the name BA.2?
The Greek letters used to name virus strains, such as delta or omicron, are chosen by the World Health Organization. Deciding where to draw the line between variants is somewhat subjective, but loosely speaking, each Greek letter represents a big branch on the coronavirus family tree.
As each new variant accumulates more mutations, it may diverge into smaller branches on the tree: subvariants.
International committees of scientists distinguish the subvariants with an alphabet soup of shorthand. All members of the omicron family, for example, have scientific names starting with the letters BA. Lineages in the delta family start with AY. Still others start with B.1.
It gets hideously complicated, since viruses multiply so rapidly — typically picking up a handful of new mutations with each cycle. The family tree now has many hundreds of branches. But all are close enough to the original coronavirus, first identified in Wuhan, China, in late 2019, that the vaccines continue to provide good protection against hospitalization and death.
How are subvariants detected?
When you go to a drive-through test site, your nasal swab is typically analyzed with a method known by the now-familiar initials of PCR (polymerase chain reaction). Those tests are not set up to detect the entire 30,000-letter genome of the coronavirus — just several key regions within this genetic code.
It works great, and it’s fast, returning a positive or negative result in a matter of hours, though you may wait longer if there’s a backlog. Such tests can also be used as a rough indicator of which variant is present.
But to make a conclusive ID of a variant, scientists must decipher the entire genome, using sequencers like the ones in Bushman’s lab at Penn. The fastest machines can still get the job done in less than a day, but such devices are far less numerous than their smaller PCR counterparts. Just a fraction of COVID-positive samples are selected to have the full viral genome sequenced. Add the time needed for follow-up analysis, and the whole process can take a week or two.
What’s different about BA.2?
The code for BA.2 differs from the original omicron variant, dubbed BA.1, by just two dozen “letters” in the virus’ 30,000-letter genetic code, Bushman said.
That may not sound like much, but some of these changes occurred in key locations, such as the “spike” that the virus uses to penetrate human cells. The impact of any one mutation is often not immediately clear, and many of them have no impact at all. But collectively, the various mutations in BA.2 seem to have made the subvariant about 30% more transmissible than the original omicron, he said.
On the plus side, BA.2 does not appear to make people sicker than the original, said Boni, the Penn State biologist. But some small fraction of infected people will nevertheless develop severe illness, more so if they are unvaccinated or immunocompromised, he said.
When millions become infected, as they did in January with the original omicron, a small fraction of that total is enough to jam hospitals.
Less of a surge?
Bushman and Boni agreed that BA.2 might cause less disease here than it did in Europe, as the United States saw many more infections in the first wave of omicron.
Echoing that sentiment this week was William Hanage, a Harvard epidemiologist who was a guest on In the Bubble, the podcast of former Biden administration COVID adviser Andy Slavitt.
“I don’t think it’s going to be as dramatic as Europe because the recent pandemic history has been really quite different,” he said. “Most of Europe has been pretty COVID-averse, whereas parts of the United States have been quite COVID-curious.”
The higher U.S. infection numbers in January were due not only to relaxed precautions, but also because the version of omicron that first emerged here was slightly different — and apparently more transmissible — than the European version, Hanage said. Hold on to your hats: The primary U.S. “flavor” in January was dubbed B.1.1, whereas the one that dominated the first omicron wave in Europe is called simply B.1.
Still, all three scientists agreed the United States could see more cases in the coming weeks, even if the rise is less pronounced than it was in Europe.
“There’s going to be a bump,” Hanage said.
What comes next in the pandemic
Even if BA.2 does not fuel a big wave here, Boni cautions that eventually, some other variant or subvariant will have a big impact — and the United States remains underprepared.
Two-thirds of the U.S. population is fully vaccinated, a big achievement considering that the virus emerged little more than two years ago.
But to guard against future variants, public health agencies should keep pushing until the percentage vaccinated reaches the high 90s, said Boni, who has served on World Health Organization committees for malaria and other disease epidemics. He knows many consider that goal impossible, given that the rate of new vaccinations has long since slowed to a trickle.
“People always say things are impossible until you do them, and then they look possible,” he said. “It’s no longer a question of science or public health or virology. It’s a question of fighting disinformation.”
He recommended that annual vaccinations be administered, just as with the flu. And for those who become ill with COVID despite vaccination, continued study is needed to improve treatments. What’s more, he said, all of it needs to be exported to the rest of the world.