MILWAUKEE — There’s been some drama in the omicron family.

BA.1 was the first sub-lineage of the omicron variant to make its mark, leading surges across the globe this past winter. But now, BA.2 — another version of omicron that’s kind of like a sister to BA.1 — is coming along to steal the spotlight.

What You Need To Know

  • BA.2, the more contagious subvariant of omicron, is poised to become dominant in Wisconsin

  • The subvariant has genetic differences from the earlier lineage, BA.1, but probably won't reinfect those who already had omicron

  • BA.2 hasn't caused a major surge in cases in the U.S. yet, and experts aren't sure it will

  • Keeping tabs on BA.2 and future variants is key to the future of the pandemic

BA.2 is even more contagious than the previously dominant versions of omicron. And it has elbowed its way into becoming the leading variant across the globe. Here in the Badger State, BA.2 is also on the rise since landing in Milwaukee earlier this year.

“It’s a matter of time that BA.2 replaces BA.1 really everywhere,” said Ajay Sethi, associate professor of population health sciences at UW-Madison. “And I don’t see why that wouldn’t happen in Wisconsin also.”


Breaking down BA.2

​When omicron first burst onto the scene, it alarmed scientists by just how different it looked from earlier variants, said Nancy Wilson, a senior scientist at UW-Madison who has been working on genetic sequencing during the pandemic.

BA.1, which was the first version of omicron to take over, had dozens of mutations that weren’t seen in the original version of the virus — including many on the key spike protein. 

That’s part of why our vaccines and treatments, which worked well at fending off earlier variants, struggled against omicron, Wilson said. It’s like you have a mental image of someone you know, and “now all of a sudden, they shave their head bald, they start putting on wild clothes and they grow a beard,” she said. “It's a lot harder to recognize who that person is.”

BA.2 shares many of the genetic changes that defined the earlier version of omicron, which is why it’s considered a subvariant instead of a totally separate variant, Wilson said. But BA.2 has also racked up many mutations of its own, Sethi said.

“They're both different from each other,” he said. “And they're both extremely different from previous variants.”

BA.2 appears to spread even faster than BA.1, with studies estimating that it’s around 30 to 50% more contagious, Sethi said. With a higher rate of infectiousness, it makes sense that BA.2 is taking over as the dominant version of the virus, he said.

But the jump between BA.1 and BA.2 isn’t as dramatic as the one between, say, delta and omicron, Wilson pointed out. That may help explain why BA.2 isn’t causing an immediate surge — and why people who recover from BA.1 seem to be pretty well protected from its sister variant.

“If you get omicron, you probably won't get the other version of it,” Wilson said. “It's a possibility, but it's not likely.”

Both of these versions of omicron — plus another lineage, BA.3 — have been around for some time, Sethi pointed out: They were all detected in South Africa back in November.

There’s no clear explanation for why BA.2, the more infectious lineage, didn’t take off before BA.1, Sethi said. It may have just been a matter of chance. But now that it’s here, BA.2 is making its mark.

“When it starts to take off, it's a moving train. It doesn't get stopped very easily,” Sethi said. “But BA.2 has been lying in the weeds for a while.”


A gradual takeover

​The BA.2 subvariant first showed up in Wisconsin at the end of January. Since then, it’s chipped away at BA.1’s dominance over the past few months, and now represents a little under half of sequenced samples in the state, according to data from the State Laboratory of Hygiene.

That’s a much slower takeover compared to when omicron first showed up and took over Wisconsin’s cases in a matter of weeks.

“It definitely hasn't been the kind of increase that we saw with omicron, where delta just plummeted and omicron really shot up,” Wilson said. “This has been a much more gradual increase.”

Sethi and Wilson both pointed out that Wisconsin is sequencing fewer samples these days, now that cases are down from their highs earlier in the year. Nationally, the CDC estimates that BA.2 is making up around 72% of new cases. 

Even as it makes its way into the variant spotlight, it’s hard to say exactly what impact BA.2 will have, experts said.

Pandemic metrics are still generally low in the U.S., but some states — especially in the Northeast — are seeing cases climb again, according to a New York Times tracker. Wisconsin, too, has seen a slight uptick recently, with positivity rates increasing “just a smidge,” Sethi said. 

We might see those numbers keep rising, as we’re faced with a more contagious omicron lineage and returning to more of our normal activities, Sethi said. Some parts of Europe have seen sizable surges since the arrival of BA.2.

But in the wake of our BA.1 wave, the U.S. is at a high level of immunity against BA.2 — from vaccination, past infection or both, Wilson said. So it’s also possible that BA.2 will become dominant without causing too much of a spike in infections.

Sethi said he expects to see a “mosaic-like pattern” of BA.2 impacts in the U.S., given its uneven rates of immunization. And he’s hopeful that our current tools for fighting the pandemic will help us manage the new subvariant — though he’s not letting his guard down yet.

“Just because it’s not leading to an immediate spike, I recognize that it can,” Sethi said. “I see BA.2 as dangerous, and something that can cause a repeat of recent history — of what we saw in the winter.”


The variants of tomorrow

​So how long could BA.2 hold on to its spot as the top variant in town?

That depends on what new versions of the virus are headed down the pipeline, experts said.

“As soon as some version comes out that's more infectious, or spreads more easily, or finds an immune niche that it can exploit, then that becomes a dominant version,” Wilson said. “It's a total competition all the time.” 

The main advantage of BA.2, like the previous variants we’ve faced, is that it’s more contagious, Sethi said. Variants may improve their spread by binding more tightly with human cells, building more viral load or replicating higher up in the respiratory tract — “closer to the exit,” Sethi said.

Future variants may get a leg up by increasing their ability to dodge the body’s immune defenses, he said. That might be even more of a concern, since until now our vaccines have at least been able to stave off severe outcomes from COVID-19.

So, as long as COVID-19 keeps spreading across the globe, we should stay on guard for future versions of the virus, experts said.

In omicron’s case, it’s possible that the variant evolved in an immunocompromised person who was battling COVID-19 for a long time — giving the virus plenty of chances to keep copying and changing itself, Sethi said. 

“When somebody's immune system is half-heartedly able to control viral replication, the virus finds a way,” Sethi said. “To quote Jeff Goldblum, right, ‘Life finds a way.’”

The virus might also have hopped into an animal host and made its way back into humans “looking like a long-lost cousin we don’t recognize anymore,” he said. Animal reservoirs for the virus are a big concern, especially given that scientists have detected SARS-CoV-2 in the widespread white-tailed deer, Wilson said.

As things stand now, Sethi said people should keep close tabs on their local pandemic data to see when they might have to change their behavior. Getting vaccinated and boosted can also keep BA.2 at bay, he said.

“The more we vaccinate, and the more we take precautions when needed, we can prevent future rises in cases from becoming really unmanageable,” Sethi said.

Though Wilson is “cautiously optimistic” that the worst of the COVID-19 pandemic is behind us, she doesn’t think we are done with the virus. Keeping up surveillance for new variants — including through proactive measures like tracking air or wastewater samples — can help us be more prepared for future spikes, she said.

“This is a tricky virus,” Wilson said. “And every time we think we're done, it starts over again.”