Highly mutated COVID variant BA.2.86 has been detected in the U.S. Why the CDC and WHO are monitoring it

The WHO on Thursday announced that it had declared BA.2.86—formerly referred to as BA.X and dubbed “Pirola” by variant trackers, after an asteroid—a “variant under monitoring,” the lowest of three levels of alert. “High flying” variants EG.5, XBB.1.5, and XBB.1.6 have been designated as “variants of interest,” of greater concern. And only Omicron persists as a “variant of concern,” the highest level of alert.

WHO has designated #COVID19 variant BA.2.86 as a ‘variant under monitoring’ today due to the large number of mutations it carries.

So far, only a few sequences of the variant have been reported from a handful of countries.
🔗 https://t.co/3tJkDZdY1V

— World Health Organization (WHO) (@WHO) August 17, 2023

Later in the day, the CDC announced that it, too, was tracking the variant, and that it had been detected in the U.S.—in Michigan, in addition to Israel and Denmark, where it had first been reported earlier in the week.

CDC is tracking a new lineage of the virus that causes COVID-19. This lineage is named BA.2.86, and has been detected in the United States, Denmark and Israel. CDC is gathering more information and will share more about this lineage as we learn it.

— CDC (@CDCgov) August 18, 2023

And on Friday, the U.K. Health Security Agency (HSA) said that the variant had been identified in England, and that it was “assessing the situation.” The patient ill with BA.2.86 is elderly and hospitalized, Raj Rajnarayanan—assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Ark., and a top COVID-variant tracker—told Fortune. They have no recent travel history, according to a risk assessment for the variant published Friday by the agency.

A case of the COVID-19 variant BA.2.86 has been identified in the UK & a number of other countries. Dr Meera Chand, Deputy Director, has said “We’re aware that BA.2.86 has been detected in the UK. UKHSA is assessing the situation & will provide further information in due course.”

— UK Health Security Agency (@UKHSA) August 18, 2023

Unlike most circulating variants, which have evolved from Omicron spawn XBB, BA.2.86 is thought to have evolved from a much earlier strain of Omicron—BA.2, which circulated in early 2022, or perhaps from the original Omicron, BA.1.1.529, which spiked cases to record highs in late 2021 and early 2022.

And it appears to be vastly different from its predecessors. So far, most widely circulating Omicron variants feature a small handful of mutations that make them slightly different from the last—usually a bit more transmissible. 

BA.2.86, on the other hand, features 30 or more mutations that separate it from other Omicron—mutations with the potential to make it considerably more immune-evasive, and able to more easily infect cells, according to Jesse Bloom, a computational biologist at Fred Hutch Cancer Center in Seattle, Wash., and top variant tracker.

That makes BA.2.86 as different from other Omicron strains as the first Omicron was from the original strain of COVID found in Wuhan in 2019, Bloom asserts in a widely cited presentation he posted online.

Because of this, “Pirola” has the potential to become the next variant the WHO awards a Greek letter to—likely Pi, hence the nickname.

“What sets this one apart from the many other Omicron subvariants is that it exhibits a large number of mutations … far more than we usually see,” Ryan Gregory, a biology professor at the University of Guelph in Ontario, told Fortune. He’s been assigning “street names” to high-flying variants since the WHO stopped assigning new Greek letters to them. 

While only six (unrelated) cases—and counting—of the variant had been identified in four countries as of late Friday, sequencing worldwide is at an all-time low.

“It’s fairly likely it’s going undetected in some other countries,” Gregory said.

The fact that the cases are geographically dispersed, with no travel history, “suggests there is established international transmission” that may have occurred only recently, the U.K. HSA said in its risk assessment. There may be a degree of community transmission in the U.K., it added.

Regarding BA.2.86, when @SolidEvidence uses the word “avalanche,” it’s not a good sign.
And here’s the 30+ Δ spike mutations (BA.2.86 vs XBB.1.5) from @RajlabN https://t.co/8UucaWlOaWhttps://t.co/m239bcQ2TB pic.twitter.com/f5f6at0iRO

— Eric Topol (@EricTopol) August 18, 2023

The cases’ wide spread and their significant similarities suggest that growth could be rapid, Ryan Hisner—a top variant tracker who discovered the second and third identified cases, in Denmark—told Fortune.

But even if BA.2.86 does spread rapidly, it may not drive hospitalizations and deaths upward, Dr. Stuart Ray, vice chair of medicine for data integrity and analytics at Johns Hopkins’ Department of Medicine, points out.

Though the highly mutated variant is “quite divergent” from other known circulating strains, “it’s unclear whether it will have a significant effect on the number of severe cases or our management/prevention strategies,” he told Fortune.

BA.2.86’s unusual origins

The unusual new variant might have equally unusual origins.

BA.2.86 likely developed in an immunocompromised patient with a long-term infection, multiple experts say. Such lengthy infections give the virus opportunity to repeatedly evolve and collect a large number of mutations—it’s likely how Delta and Omicron came about.

But variants from immunocompromised patients rarely spread—which is why Hisner was taken aback when he spotted the variant, first identified in a patient in Israel, in Europe.

Because the infected Israeli patient wasn’t immunocompromised, he knew that the variant had likely already made the leap from someone with a sub-par immune system to hosts with normal ones. Hisner wasn’t sure when more sequences would appear, “but I figured we would see at least a few eventually,” he said.

“But when they showed up in Denmark, I was really taken aback.”

Can BA.2.86 out-compete leading variants?

Three main questions remain: how the variant’s mutations will affect symptoms and severity, if it will take off anywhere (or everywhere), and how new XBB.1.5 COVID vaccines—slated for U.S. release in September—might hold up (in addition to our existing immunity).

The significant number of mutations in BA.2.86 portends significant changes in immune evasion, the U.K. HSA said in its Friday report. But immunity is broader than just antibodies, Bloom points out. While antibody immunity to COVID, from either infection or vaccination, lasts only three to six months on average, T-cell immunity is thought to last much longer.

“Even if a highly mutated new variant like BA.2.86 starts to spread, we will be in a far better place than we were in 2020 and 2021, since most people have some immunity” to COVID, he recently wrote.

Regardless of the vaccine’s performance against it, treatments like COVID antiviral Paxlovid that don’t target the virus’s highly mutated spike protein should still work well, according to Rajnarayanan.

All scenarios are possible. But even if BA.2.86 were to take off in the U.S. or worldwide, “I’d be very surprised if things get as bad as they did in that first winter, or during the Delta era or that first BA.1 wave” in late 2021 and early 2022, Hisner said.

U.S. COVID deaths, hospitalizations continue upward trend

The CDC’s latest U.S. COVID data on Friday showed a continued upward trend in hospitalizations, which saw a 14% rise from July 30-Aug. 5, the most recent period for which data was available. Deaths, too, were up—8% from Aug. 6-12. “Eris” EG.5 lead sequenced domestic cases, comprising an estimated 20%, followed by “Fornax” FL.1.5.1, estimated to be responsible for 13% of cases.

Globally, reported COVID cases were up 63% from mid-July through mid-August compared to the month prior, the WHO said Thursday in a situation report. It cautioned that “reported cases do not accurately represent infection rates due to the reduction in testing and reporting globally.”

During that time period, only 44% of countries reported any COVID infections to the WHO—a number that could include countries that reported only one case.