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'Stealth' omicron cases rising in the US: Here's what we know.

illustration of several coronavirus particles
(Image credit: Yuichiro Chino via Getty Images)

The omicron subvariant BA.2, also known as "stealth" omicron, has steadily grown more common in the U.S. since it was first detected in the country in January, but that doesn't mean it will trigger a huge new wave of infection. That said, some experts are still concerned that such a surge could occur.

Here's what you should know about the rise of stealth omicron in the U.S.:

Scientists first identified the subvariant back in December 2021, Live Science previously reported. At that time, they discovered that the original omicron lineage had split in two. They designated the original version of the variant as BA.1 and its genetically distinct spin-off as BA.2. 

(Later, another sublineage was identified and named BA.3, and BA.1 spawned another sublineage known as BA.1.1, according to NewsMedical (opens in new tab). BA.1.1 very closely resembles the original omicron but carries a substitution in the gene that codes for its spike protein.)

BA.2 became known as "stealth" omicron because researchers raised concerns that the subvariant might be more difficult to track than the original omicron variant. 

Related: Coronavirus variants: Facts about omicron, delta and other COVID-19 mutants 

Unlike stealth omicron, BA.1 bears a deletion in the gene that codes for its spike protein, which the virus uses to infect cells. This specific mutation causes PCR tests to display an error message — "S gene target failure" — when they detect the original omicron, and this error message made the omicron variant easy to track when it first emerged, Live Science reported. This error message did not affect the ability of PCR tests to detect a COVID-19 infection, because the tests scan for multiple coronavirus genes.

BA.2 doesn't have this mutation, so it doesn't generate the same error message. That meant that, at least on PCR tests, stealth omicron looks similar to the delta variant or other coronavirus variants without the spike mutation. So, to correctly identify a stealth omicron case when there were several variants circulating, scientists would need to complete a full genomic analysis. 

Now, however, omicron subvariants account for the vast majority of new cases worldwide. With little to no cases caused by delta or other variants, the so-called stealth variant should now be easy to spot, The New York Times reported (opens in new tab).

BA.2 was detected at low levels in the U.S. in January, Live Science previously reported, but cases have ticked upward since then. Between Jan. 30 and Feb. 5, the subvariant accounted for about 1% of the new coronavirus cases captured by the Centers for Disease Control and Prevention's (CDC) national genomic surveillance system, the agency reported (opens in new tab). That number jumped to about 7% toward the end of February and then up to nearly 14% in the first week of March, the CDC estimated.

Between March 6 and March 12, BA.2 accounted for an estimated 23.1% of new coronavirus cases in the country, the CDC reported. In the same week, BA.1 accounted for 10.8% of cases, and BA.1.1 made up the other 66.1%.

So, as of mid-March, BA.2 cases continue to grow more common in the U.S., but they've yet to edge out cases caused by other versions of omicron. By contrast, in other countries — including the Philippines, India, Denmark, Singapore, Austria and South Africa  — BA.2 quickly outpaced BA.1 and had become the dominant subvariant by January, NewsMedical reported.

Related: 20 of the worst epidemics and pandemics in history 

BA.2 may follow the same trajectory in the U.S. and soon emerge as the dominant subvariant. But if it takes over, will the subvariant trigger a massive new wave of infection? Not necessarily, the Times reported.

That's partially because, although BA.2 seems to spread (opens in new tab) more easily (opens in new tab) than the original omicron, previous infections with BA.1 seem to provide strong protection against infection with BA.2, "at least for the limited period for which data are available," according to a Feb. 22 statement from the World Health Organization (WHO) (opens in new tab)

Vaccines seem to offer similar levels of protection against both subvariants, although in general, all versions of omicron can cause breakthrough infections, the Times reported. The vaccines still offer strong protection against severe disease and hospitalization from omicron, and booster shots strengthen that protection, data from the U.K. government suggest (opens in new tab).

However, some experts are still wary of a potential surge driven by BA.2. Although millions of U.S. residents caught omicron during the recent winter wave and may now be protected from BA.2, it's unclear how long that protection lasts, Jeffrey Shaman, an epidemiologist at the Columbia University Mailman School of Public Health, told The Washington Post (opens in new tab). The relaxation of mask mandates and other precautions could also hasten BA.2's spread, while variable vaccination rates around the country could lead to hotspots of severe disease and hospitalization, should a surge occur, the Post reported.

Preliminary data from the U.K. (opens in new tab) hint that BA.2 isn't more likely to cause severe disease and hospitalization compared with BA.1, but this finding still needs to be confirmed. A recent study in hamsters (opens in new tab) suggested that the stealth variant does trigger more severe disease than BA.1, but it's not clear whether these findings in hamsters would carry over to humans, the Times reported.

For now, BA.2 appears to be spreading more slowly in the U.S. than it has in other countries, for reasons that aren’t entirely clear, Debbie Dowell, chief medical officer for the CDC’s covid-19 response, said in a briefing Saturday (March 12) for clinicians sponsored by the Infectious Diseases Society of America, the Washington Post reported.

"The speculation I've seen is that it may extend the curve going down, case rates from omicron, but is unlikely to cause another surge that we saw initially with omicron," Dowell said.

Originally published on Live Science.

Nicoletta Lanese
Staff Writer

Nicoletta Lanese is a staff writer for Live Science covering health and medicine, along with an assortment of biology, animal, environment and climate stories. She holds degrees in neuroscience and dance from the University of Florida and a graduate certificate in science communication from the University of California, Santa Cruz. Her work has appeared in The Scientist Magazine, Science News, The San Jose Mercury News and Mongabay, among other outlets.