Cases of the Omicron variant are on the decline in U.S. and worldwide—but a different version of Omicron is now gaining traction.
This so-called stealth variant, officially known as BA.2, is armed with even higher transmission potential, and possibly a greater ability to evade the immune response, than the original Omicron, leading experts to fear it could further prolong the COVID-19 pandemic.
The World Health Organization does not yet consider BA.2 to be a distinct “variant of concern” but is continuing to monitor its spread. BA.2 is beginning to replace the original Omicron strain in many countries. It is now the dominant variant in Denmark, which recorded more than 50,000 new infections in just one day last week.
BA.2 also appears to be the major Omicron lineage in parts of India and the Philippines. It has already caused about 250 cases in the United States and been identified in more than half the states.
The BA.2 subvariant likely arose from a common ancestor around the same time as the original Omicron, also known as BA.1, so it is not a descendent but a sibling, says Cornelius Römer, a bioinformatician at the Biozentrum of the University of Basel in Switzerland.
“I would hypothesize that BA.1 dominated first simply because it started spreading earlier, and now BA.2 is catching up,” says Jesse Bloom, an evolutionary virologist at the Fred Hutchinson Cancer Research Center and a Howard Hughes Medical Institute investigator.
However, BA.2 has been sometimes dubbed a stealth variant because it is missing key mutations in its spike protein that are necessary for rapid PCR tests to distinguish it from previous variants, such as Delta. This difference also may be why BA.2 escaped attention earlier.
In fact, the two Omicron lineages have greater evolutionary divergences from each other than the differences between the original virus and the Alpha variant, the first variant of concern. “BA.2 shares over 30 mutations with BA.1, but it also has 28 unique mutations,” says Shay Fleishon, an evolutionary geneticist and advisor to the Central Virology Laboratory in Israel.
This suggests that the common ancestor of both Omicron subvariants spread for quite some time, evolving into distinct subvariants before BA.1 was detected by a stroke of luck: A pair of mutations deleted two amino acids from its spike protein, making BA.1 easier to distinguish from Delta in rapid tests.
Still, BA.2 is “just as detectable by PCR as any other variant,” says Römer, referring to the “gold standard” tests that rely on time-consuming but highly accurate genetic techniques.
Most of the differences between BA.2 and BA.1 are in the spike protein of the virus, which it uses to anchor to and infect human cells. BA.2 also has a large number of mutations in other parts of its viral sequence that are not well understood.
Early estimates by Denmark’s State Serum Institute suggest BA.2 is about 50 percent more transmissible than the previous BA.1 strain. The Danish study, which is not yet peer reviewed, looked into the way COVID-19 spread in 8,541 households between late December and early January. About a quarter were BA.2 cases, and the data show that even fully vaccinated people are more susceptible to catching BA.2 than BA.1.
The United Kingdom Health Security Agency also estimates that BA.2 is more transmissible, though it puts the figure at roughly 30 percent higher than BA.1.
The genetic basis behind BA.2’s transmission advantage is not yet understood, says Bloom, who has combined computational and experimental methods to study the evolution of the SARS-CoV-2 virus and understand how specific mutations influence infection.
But the good news is that experts think it’s unlikely BA.2 will cause a spike in severe infections.
Another study that is not yet peer reviewed bolsters the case that the BA.1 version of Omicron causes less severe disease than previous variants, especially Delta; only half a percent of 52,297 Omicron cases in Southern California required hospital admissions. Similarly in the U.K., most admissions to the intensive care unit were caused by Delta until January 19, 2022, when the most recent data are available.
- Courtesy National Geographic
