What is ‘stealth Omicron’? The rise of the subvariant is alarming some scientists who say it needs its own Greek letter

January 21, 2022, 9:24 AM UTC

The Omicron subvariant BA.2, nicknamed the “stealth Omicron,” appears to be outpacing other substrains of Omicron in some regions of the world, raising fears that the even more transmissible version of Omicron could spark larger COVID-19 waves globally.

The World Health Organization (WHO) says that Omicron, which is also referred to as B.1.1.529, has three main substrains: BA.1, BA.2, and BA.3. As of Dec. 23, the WHO reported that over 99% of the cases it sequenced were BA.1. But now the rise of BA.2 in Denmark and elsewhere suggests that BA.2 may outcompete BA.1.

On Thursday, Denmark reported that the BA.2 substrain of Omicron accounts for almost half of the country’s cases and is quickly displacing BA.1, the original Omicron strain. Denmark reported that in the two weeks from late December to mid-January, BA.2 has gone from accounting for 20% of Denmark’s COVID-19 infections to making up 45%. Over that same period, Denmark’s COVID infections have shot to record highs. Denmark is recording over 30,000 new cases per day this week, 10 times more cases than peaks in previous waves.

Denmark’s government also said the strain is spreading quickly in countries like the U.K., Norway, and Sweden. Meanwhile, scientists in places like France and India warn that the BA.2 variant is quickly spreading and may outpace other Omicron strains.

But Danish authorities also urged the public to not read too much into BA.2’s rise at this point.

“Initial analysis shows no differences in hospitalizations for BA.2 compared to BA.1,” Denmark’s Statens Serum Institut, a government-run infectious disease research center, said in a statement on Thursday. “It is expected that vaccines also have an effect against severe illness upon BA.2 infection.”

Even with its recent surge in cases, Denmark is easing restrictions because the number of COVID patients needing intensive care is decreasing. A Danish study found this week that the risk of going to the hospital has been 36% lower for people infected with Omicron, compared to the Delta variant.

Researchers note that the BA.2 version of Omicron may have 28 unique mutations compared to BA.1, even as the two Omicron strains share 32 mutations.

Denmark says it is too early to tell what BA.2’s mutations mean. “Such differences can lead to different properties, for instance, concerning infectiousness, vaccine efficiency, or severity. So far there is no information as to whether BA.1 and BA.2 have different properties,” the Statens Serum Institut said.

When scientists discovered the BA.2 Omicron substrain in South Africa in late November, they believed it was going to be more difficult to track than the original Omicron variant. Omicron’s original strain, BA.1, has a mutation—the deletion in the “S” or spike gene—that shows up on PCR tests, making it easy to tell if someone is infected with Omicron. BA.2 does not have that same mutation, earning the strain its “stealth Omicron” nickname.

But now experts are pushing back on the notion that the substrain is as stealthy as it first seemed. The experts say the BA.2 strain does show up on PCR tests, just not necessarily in the same way as Omicron BA.1.

“BA.2 is detectable by PCR…Depending on the PCR test used it may not look like BA.1 (the other Omicron). But it will still give a positive result,” Cornelius Roemer, a computational biologist at Switzerland’s University of Basel, wrote on Twitter. “[It’s] frustrating to see falsehood about non-detectability still around.”

Still, the variant is raising some alarms because there are early signs that it may be even more transmissible than the original strain of Omicron.

“[Consistent] growth across multiple countries is evidence BA.2 may be some degree more transmissible than BA.1,” Tom Peacock, a virologist from the Imperial College of London, tweeted on Wednesday.

Some researchers believe that BA.2 is so distinct from Omicron’s original strain that the World Health Organization should label it a variant of concern—reserved for variants that demonstrate increased transmissibility, among other factors—and give it its own name.

“I think the responsible thing to do is to relate to BA.2 as a completely different variant, outcompeting BA.1,” Shay Fleishon, a researcher affiliated with the Israeli government’s Central Virology Laboratory, wrote on Twitter. “Oh and if someone in the WHO is here—The letter Pi is still waiting. Just saying.”

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