New COVID variant on the horizon shows virus’ rapid evolution, as new booster nears

Paul Sisson | San Diego Union-Tribune

The U.S. Centers for Disease Control and Prevention expects a refreshed booster vaccine to be available next month, but it remains to be seen whether the new shot will be able to snipe a highly mutated coronavirus variant that is just starting to appear.

Nicknamed “Pirola” by scientists on social media, this new bug’s technical name is BA.2.86, which makes it a descendant of the Omicron virus that first appeared in late 2021, causing the largest surge in cases of the COVID-19 pandemic.

But the latest variant is said to have more than 35 additional mutations than XBB 1.5, the variant that will be included in this year’s booster, according to a risk assessment from the U.S. Centers for Disease Control and Prevention.

Experts are recommending that people wait for the newest booster when it becomes available — even though, as with each new yearly dose, it remains uncertain how well the immunity it induces will match up with the latest coronavirus strains.

At the moment, many are building immunity the old fashioned way, by becoming infected. As it has every summer since 2020, coronavirus has spread broadly in San Diego and across the nation due to summer travel and large gatherings.

The latest research shows that, while the public was clearly determined to make 2023 its first post-COVID year, the virus is continuing to evolve at a pace that makes another round of illness a near certainty this fall.

Pirola was first identified on July 24, more than one month after the U.S. Food and Drug Administration approved XBB 1.5 — widely called “Kraken” — as the single strain included in the booster that faces approval next month. At the time, EG.5, another child of Omicron, had begun circulating widely. Recent statements from drug manufacturers say that their boosters are very effective against this viral version which has been nicknamed “Eris.”

Eris, though, differs little from Kraken. Pirola, by comparison is a much bigger leap, with the CDC concluding that the “number of genetic differences (between Pirola and Kraken) is roughly of the same magnitude as seen between the initial Omicron variant and previous variants such as Delta.”

It is hard, at the moment, to know just how well the new booster will match with Pirola, as it is not yet the dominant strain that is infecting people in the real world. The CDC’s assessment, published Wednesday, notes that, to date, only nine copies of the subvariant’s genetic sequence had been reported, with just two of them in the United States.

It remains to be seen, then, whether or not Pirola will outcompete Eris and become the dominant coronavirus nationally or internationally.

So far, there is no evidence that Pirola is circulating in San Diego County.

San Diego’s most-recent coronavirus lineage report, updated last week for the first time since June, lists Eris as the dominant circulating strain, though wastewater samples analyzed to make the report were collected on Aug. 6 or earlier. That means there are weeks of additional viral churn in the community that have not yet been accounted for.

Highly-cited immunologist Shane Crotty of the La Jolla Institute for Immunology, whose work was pivotal in mapping how the immune system interacts with pandemic coronavirus, was not terribly interested in handicapping that particular race when asked for his opinion this week.

“You can look at the available data and tell that some variants are more interesting than others because of the number of mutations that they have and where those mutations are located,” Crotty said. “But how problematic they’re going to be really is dependent on just watching those case numbers.”

He noted that human immune systems have now had several encounters, whether through vaccination or infection, with this particular germ, and it’s difficult to say how that complex immunity will play out against a highly-mutated threat.

“There is somewhat different immunity to different variants, so that can make some people more susceptible to a new variant but other people not more susceptible,” Crotty said.

The FDA’s decision to unleash the Kraken for this year’s vaccine, but not include a second viral reference as was the case for last year’s booster, is making some a little uncomfortalbe, especially given Pirola’s recent reminder of just how much additional evolution this virus can still pull off.

T. Ryan Gregory, an evolutionary biologist at the University of Guelph in Ontario and one of the first to affix the Pirola nickname to BA.2.86 on X, formerly known as Twitter, said in an email Friday that “targeting one variant is perhaps not particularly forward-looking as that variant will be largely gone by the fall.”

“It might have been wise to look at which mutations and combinations of mutations are evolving independently in multiple lineages and aim at those,” Gregory said.

But it’s not clear that including a second reference strain in the vaccine would have moved the public to action. It certainly didn’t in 2022 when the current two-strain “bivalent” booster arrived. Vaccination registries show that most people are skipping boosters all together.

According to the CDC, while 69 percent of Americans completed their initial two-dose vaccination series, just 17 percent are up-to-date with last year’s booster dose. The numbers are a little better in California with nearly 73 percent initially vaccinated and 21 percent considered up-to-date. San Diego County has done better still, achieving an 81 percent initial vaccination rate with 22 percent following through with their booster shots.

But that’s still less than one in four getting boosted, even in a town that is home to organizations such as LJI and Scripps Institute whose scientists have been intimately involved in prosecuting the COVID-19 pandemic from the beginning.

Low uptake rates suggest that large swathes of the population aren’t seeing the value of getting boosted. But Dr. Robert “Chip” Schooley, an infectious disease specialist at UC San Diego, said that perspective can be short sighted, especially for those with increased risk of serious COVID complications.

It’s important to remember, he said this week, that natural and vaccine-induced immunity wanes over time, and a big proportion of the benefit of a booster shot is triggering the immune system’s memory cells to churn out a fresh crop of protective antibodies and T-cells which are able to hunt down a relatively wide range of cross-related viruses.

Vaccination then spurs a fresh set of infection-fighting troops, some of which will be made to fight the strain included in the vaccine but also accompanied by allies patterned after other coronavirus types.

“If you are in a risk group, you know, older, have all the risk factors we’ve been talking about with things like obesity, cardiovascular disease, diabetes, even if you had COVID this summer, you really don’t want to miss the chance to give your immune system another opportunity to play around with the virus and get a little bit broader immunity and get a little bit stronger,” Schooley said.

Having received his bivalent booster in the spring, and having not gotten sick this summer, Schooley said he intends to get the new booster this fall.