WHO keeping closer watch on BA.2.86 strain as a dearth of data makes predictions difficult

The World Health Organization has notched up the status of the coronavirus strain BA.2.86 and its offshoots, naming it a “variant of interest,” although the organization says the current risk from this family of viruses appears to be low.

Previously, the organization had been following this lineage as a “variant under monitoring.”

WHO also has XBB.1.5, XBB.1.6 and EG.5 classified as variants of interest. There are no current variants of concern, the highest designation.

BA.2.86 first turned up in the US in August and is now the third most common variant, causing an estimated 1 in 11 new cases of Covid-19 here, according to the latest update of the US Centers for Disease Control and Prevention’s variant tracker. The prevalence appears to have tripled in the past two weeks, although a variant’s growth is often overestimated in the first few weeks after it shows up in the CDC’s monitoring.

But if BA.2.86 doesn’t appear to be such big deal, why would WHO upgrade it?

“We’ve seen a slow and steady increase in its detection around the world,” said Dr. Maria Van Kerkhove, WHO’s technical lead on Covid-19, in a video posted on social media. “By characterizing it as a variant of interest really helps to promote surveillance for these types of variants around the world as well as to stimulate research” to understand whether they cause more severe disease or are more immune-evasive, she said.

A slow build

BA.2.86, which some virus watchers have dubbed Pirola, triggered a flurry of research when it came to the world’s attention over the summer because it shared many of the characteristics that caused BA.1, the original Omicron strain of the coronavirus, to spread like wildfire, prompting hospitalizations and deaths to spike globally.

With more than 30 mutations to its spike proteins, BA.2.86 was so genetically distinct from previous versions of the virus that causes Covid-19 that scientists had feared it might completely slip past the immunity of vaccinations and infections to fuel another wave of infections.

But perplexingly, BA.2.86 never really took off the same way the first Omicron did. Some studies suggested that as it developed all its new mutations, this variant lost some of its ability to infect our cells, slowing its growth.

Other studies found that it didn’t completely evade the body’s immunity and that the current Covid-19 vaccine, which carries instructions on fighting the XBB.1.5 subvariant, offered some protection against it, which was good news.

Variant hunters have tempered that optimism, however, by warning that even if the original BA.2.86 virus was more lamb than lion, it was still evolving, and one of its descendants might gain back enough fitness to become a force to be reckoned with.

Indeed, BA.2.86 continues to evolve and send fitter offspring into the world, says Dr. Jesse Bloom, a computational virologist at the Fred Hutchinson Cancer Center in Seattle.

Bloom says work by researchers at Columbia University and in China has shown that the JN.1 subvariant has one change to its genetic code that makes it more capable of escaping our immune defenses, although the difference is modest: about a twofold decrease in the ability of our antibodies to neutralize the virus.

Still, that tweak seems to have been enough to give it a growth advantage over its predecessor.

“As far as fitness, what we can see is that JN.1 is increasing in numbers faster than its parent, BA.2.86,” Bloom said.

At the same time, the distantly related XBB family of viruses, which now includes several faster and fitter descendants like HV.1, is rising in prevalence. HV.1 is currently the dominant lineage in the US, according to the CDC, causing an average of about 1 in 3 new cases of Covid-19.

“From a scientific perspective, all these variants are kind of currently on the move, and I could see either family spreading. What exactly it’s going to mean, for Covid case counts and Covid disease burden this winter, is hard to say,” Bloom said.

Dearth of data makes predictions difficult

Overseas, a number of countries have seen case numbers go up as BA.2.86 and JN.1 have spread, said Dr. Michael Osterholm, who directs the Center for Infectious Disease Research and Policy at the University of Minnesota.

“In Europe, it has been associated in several countries with big increasing number of cases, and other countries it hasn’t, so what gives?” he said.

Europe used to be a good barometer for what Covid-19 might do in the US, but immunity, behavior and surveillance are so different from country to country now that it’s tough to know what might happen here.

One big problem is that data is dwindling, says Dr. Peter Hotez, a pediatric infectious disease specialist at the Baylor College of Medicine and Texas Children’s Hospital who developed a vaccine against Covid-19.

“It’s harder to read the tea leaves than it used to be because we’re not doing as much surveillance, so you have to base [predictions] on a hodgepodge of things like wastewater and hospital admissions and percent positivity,” Hotez said.

Still, taking into account the signs we can see, Hotez says, there’s reason for caution in the weeks ahead.

Covid-19 hospitalizations, which had been dropping, have started to nudge back up again. Last week, more than 18,000 Americans were hospitalized with Covid-19, about a 10% increase over the week prior, according to CDC data. Nationally, coronavirus levels in wastewater are high and appear to be increasing, which may portend rising case numbers.

At the same time, a paltry 16% of American adults and just 6% of kids have gotten the latest Covid-19 vaccine, which studies have shown robustly boosts antibodies against the XBB family of viruses and provides some protection against the BA.2.86 family, though to a lesser extent.

A recent study by microbiologist and immunologist Dr. David Ho and his lab at Columbia University found that although last year’s booster – which carried instructions to stave off two versions of the virus that causes Covid-19, the original strain and BA.5 – didn’t seem to really retune our immunity to fight off the latest variants the way scientists hoped it would, this year’s single-strain shot really is all that and a bag of chips.

The strategy of going back to a single-strain shot and boosting against the strongest leading variant seems to have paid off, raising antibodies about 27-fold against the current crop of variants, including JN.1.

Bloom says this is great news because it means the strategy of tweaking the recipe for the Covid-19 vaccine each year should continue to help blunt the worst outcomes of infections, as long as people get their shots.

But the low uptake means there’s a bigger pool of adults and children who may be susceptible to breakthrough infections and reinfections with Covid-19.

“I think we could see the numbers start to increase as we head into the holiday season,” Hotez said. “We’ve got to redouble our efforts to get more Americans to take this booster. I think that’s the single most important action item right now.”

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