There’s yet another twist in the pandemic: The omicron variant of SARS-CoV-2, the virus that causes Covid-19, now has a “subvariant” that seems to spread more quickly than any other version of the coronavirus to date.
The good news for now is that vaccines still appear to protect against it. But because it’s so transmissible, scientists are racing to figure out what harm it could cause.
The original omicron variant, which scientists call BA.1 or B.1.1.529, was until recently the most transmissible known version of the virus. In many countries, it caused some of the steepest and tallest peaks in new Covid-19 cases. But we now know that one of its descendants, known as BA.2, can spread faster still, and may soon become the dominant version of the virus.
The subvariant is already circulating in at least 69 countries, including the United States, according to the World Health Organization. “BA.2 is more transmissible than BA.1, so we expect to see BA.2 increasing in detection around the world,” said Maria Van Kerkhove, the technical lead for Covid-19 at the WHO, during a press conference on Tuesday.
While it’s not distinct enough to be classified as an entirely new variant with its own Greek name, BA.2 has about 20 mutations that set it apart from its parent BA.1. Annoyingly, it does not contain a mutation that distinguishes omicron from other variants in genetic PCR tests, so it’s harder to tell apart from, say, delta. That’s why some researchers have described BA.2 as “stealth omicron.”
To be clear, routine coronavirus tests can tell when a person is infected with the omicron subvariant. But because of the missing mutation, “you don’t know what you’re looking at, whether it’s BA.1 or BA.2,” or a different variant altogether, said Gregory Poland, a professor of medicine and infectious disease at the Mayo Clinic. As a result, identifying BA.2 infections usually requires more extensive genetic sequencing — and in parts of the world where that’s less common, it may be spreading undetected.
BA.2 is an iteration, not a revolution. It’s no surprise that the coronavirus is continuing to evolve: The more people the virus infects, the greater the chances that it will mutate. And with omicron infections already peaking in many countries, BA.2 might not trigger major new spikes. But some estimates show that it’s more than 1.5 times as transmissible as BA.1, and that could slow down the decline in cases.
The omicron wave might be even slower to recede because countries are also relaxing pandemic restrictions; for example, by allowing gatherings to resume and lifting face mask requirements. The virus isn’t making things easy, and our actions may make things worse.
BA.2 spreads quickly, but vaccines remain effective against severe Covid-19
Viruses like SARS-CoV-2 mutate all the time as they replicate. When a virus acquires enough distinct mutations, it’s categorized as a variant. But if the changes aren’t that drastic, a mutated virus might be described as a subvariant, like BA.2.
Its rise brings another round of frustrating unknowns, but some answers are already starting to emerge.
Denmark experienced one of the earliest BA.2 surges. The subvariant accounted for almost half of all Covid-19 cases in the country by the end of January — even though more than 80 percent of Denmark’s population completed their initial course of Covid-19 vaccines, and more than 60 percent have received a booster so far. Denmark peaked at around 45,000 new cases (measured as a seven-day average) on January 27.
Omicron fueled the recent Covid-19 surge in Denmark in part because it can dodge some of our immune system’s defenses, said Frederik Plesner Lyngse, a postdoctoral researcher at the University of Copenhagen. “One of the reasons why we think omicron took over so fast in Denmark is we actually saw it having strong immune-evasive properties,” he said.
But among the versions of omicron, BA.2 quickly dominated, according to a preprint paper he co-authored that has not yet been peer-reviewed. “When we look at BA.1 compared to BA.2, we really see that BA.2 is intrinsically more transmittable,” Lyngse said.
Another study from the United Kingdom also found that for BA.2, “the apparent growth advantage is currently substantial.”
Vaccines still appear to reduce the spread of BA.2 and cut the rates of severe disease. BA.2 spread most extensively among those who were not vaccinated against Covid-19.
Many countries have already experienced a very sharp increase in cases from omicron, followed by an equally sharp drop. But the higher transmission rate of BA.2 could drag out the omicron wave in some places.
“I think it’s going to be slower and longer to get down to the base level we would have otherwise,” Poland said. “This all but guarantees that the people who are unvaccinated, and haven’t been infected yet, will be.”
There are important mysteries left to solve about BA.2
Scientists are still trying to pick apart the reasons for BA.2’s rapid transmission. They have their suspicions: Many of the mutations in BA.2 are in parts of the virus that the immune system usually likes to target, so changes that disguise those regions may allow the pathogen to escape detection.
However, it’s not clear whether BA.2 is different enough to cause reinfections in people who have been infected with BA.1. In other words, if you were infected with the original omicron variant, scientists don’t know if you can then get the omicron subvariant.
These aren’t easy questions to answer, in part because scientists can’t predict changes to the disease simply by studying changes in the genetic code or the physical structure of the virus.
In variants like delta and omicron, mutations work together, ratcheting up transmission rates beyond what any individual mutation could cause, explained Poland. So variants are more than the sum of their mutations, and scientists have to observe them in the real world to understand how they behave. Learning how the virus spreads and does damage is critical to halting transmission and treating infections.
Another mystery is where BA.2 came from. It may have been around since the beginning of omicron: Some of its earliest known genetic sequences were uploaded to an international database from the Philippines and from South Africa in November 2021. BA.2 may have branched off from BA.1 shortly after omicron began circulating widely.
Omicron itself has no known direct ancestor, though — it’s not a direct descendant of delta or beta, for example — and its genome shows that it comes from a far more remote branch of the SARS-CoV-2 family tree than other variants.
Some scientists theorize that omicron and its subvariants may have had an animal host before jumping into humans. Others think the evidence points to a rare type of mutation event known as recombination, in which an individual is infected with two versions of the virus at the same time, leading the pathogens to swap parts and produce an entirely different variant. It may also be the result of an infection in a person who was not able to fight off the virus quickly, giving it an unusually long time to replicate, mutate, and hone itself against the immune system.
Figuring out how variants keep cropping up could help close off routes for future changes, or at least help scientists learn where to look so they aren’t caught off guard. The rise of BA.2 is yet another reminder of why we need more vigilance against Covid-19, even when cases are declining. Otherwise, the twists will keep coming.