What to know about BA.2, the new omicron subvariant

Ominously nicknamed the “stealth variant,” the latest COVID-19 viral version arrives in the United States with the usual uncertainty that accompanies every iteration of the virus.

Scientists don’t know enough to predict exactly what the latest might do.

This one is just a little different from the omicron strain only now subsiding. Officially dubbed BA.2, it may spread a little more easily than now-waning omicron, some scientists think, and may be a little more effective at eluding the protections vaccines and previous infections provide. So far, indications are it doesn’t make people any sicker than omicron — which still wound up spiking hospitalization and death rates simply because it affected so many more people.

» READ MORE: Philadelphia’s ability to track COVID-19 variants — and the nation’s — is hobbled by a lack of resources

The pattern of a new type of COVID-19 emerging in a far-off country and days later emerging in the United States is prompting an all-too-familiar sense of déjà vu — as do the unanswered questions.

Early evidence out of Denmark, where the subvariant now accounts for 65% of all cases, points to a strain of COVID-19 that spreads more effectively than the original omicron variant. That variant’s likelihood of spreading within a household with one affected member is about 29%, compared with 39% for BA.2. It appears the risk of infection for vaccinated people is higher as well.

A British study, though, found vaccines appeared to be just as effective on the subvariant as on the original omicron.

Vaccinated people are less likely to spread the subvariant, the Danish data suggested, than original omicron.

An earlier Danish study showed no increase in rates of hospitalizations as the new subvariant spread.

“We don’t know whether or not this is going to be a second surge or it’s just going to be something that circulates at a lower level,” said Paul Planet, an attending physician in the division of infectious diseases at Children’s Hospital of Philadelphia and head of the hospital’s sequencing lab.

Frederic Bushman, chair of microbiology at University of Pennsylvania’s Perelman School of Medicine, was somewhat more confident that the subvariant won’t be very disruptive. Bushman is codirector of the Penn Center for Research on Coronavirus and Other Emerging Pathogens, one of the labs that works to identify the COVID-19 variants circulating in the region.

“I think from what I’ve been seeing there’s not much reason to think there will be a big change,” he said. “Again, it’s early days and I could change my tune tomorrow.”

Viruses are sloppy reproducers, and genetic differences between generations are normal, Bushman said. Sometimes those differences can be significant, creating an entirely new variant. The omicron variant’s large number of mutations made it much more transmissible and better at evading the immune response from vaccines than other strains of COVID-19. Often, though, subvariants, which don’t have enough differences to be considered a new variant, have genetic differences that do little to change how the virus spreads and sickens people.

“They could have indistinguishable effects on people,” Bushman said, “but they are genetically distinguishable.”

The Penn lab’s dashboard, for example, tracked six different versions of the delta variant. Danish studies of BA.2, which have been among the most extensive, showed significant genetic variation between BA.2 and the omicron variant that recently surged in the United States, BA.1, but so far, there isn’t evidence that the changes translate into significantly different effects on people infected.

So far, BA.2 cases makes up just 8% of all COVID-19 cases nationwide, the New York Times reported. Its presence hasn’t been confirmed in the Philadelphia region, but CHOP’s lab is sequencing samples now that may be BA.2 infections, Planet said. The lab should know for sure in about a week, he said. It will likely be another week or two after that before it’s clear whether the subvariant will noticeably change the downward trajectory of case counts in the region.

BA.2 might have no impact on case counts in the region. Or cases could continue declining, but at a slower rate than they have been recently. It’s also possible cases could start rising again.

Not really. The original omicron variant was easy to identify because it lacked one of three genes used in PCR tests for COVID-19. BA.2 does not have that dropped gene. Because COVID-19 cases are now overwhelmingly from the omicron variant, Planet said, any COVID-19 test without that mutation has probably spotted BA.2. There are already COVID-19 samples the lab has that don’t have the dropped gene. Planet expects they will be confirmed as the subvariant.

The entire pandemic has been an exercise in educating the public about the scientific method and why it takes time, Bushman said. Evaluating the risk of a new variant, or the effectiveness of a possible COVID-19 treatment, requires hard evidence that there is a clear difference between two variants, or between treatments.

“It’s evidence-based medicine, simple statistics. Have a control. Measure the outcome. Decide what you’re going to measure,” he said. “These painful and annoying statistical procedures that tell you whether you’re actually accomplishing anything or not.”

» READ MORE: Omicron variant is likely to come to Philly region. This Penn lab may be the first place that spots it.

There is evidence of BA.2′s effects from Denmark, South Africa, and Britain, Planet said. But the subvariant may affect us differently because our population is different.

“It has been found in the U.S., estimated at a very low percentage,” he said. “We have essentially no data about what it’s doing here yet.”

The frequency of COVID-19 strains isn’t predictable, Planet said. Researchers are trying to predict what the next variants might be, much as scientists use flu-strain predictions to develop the annual flu shot.

Knowing how severe a variant might be or what organs it will hit hardest is difficult, he said, but one constant is that a virus’ job is to spread. Unfortunately, he said, that may mean the virus will get better at evading immune defenses.

“Luckily so far our vaccines have remained pretty successful in mitigating effects, especially mitigating the severe effects of these, but it’s concerning.”