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'Stealth' omicron is in the US. Here's what we know about it.

medical worker in protective clothing giving a nose swab to a female patient
(Image credit: Alessandro Biascioli via Getty Images)

A stealthy version of the omicron variant has been detected in the U.S., but so far, it makes up a very low proportion of the overall cases in the country.

This version of the variant, called BA.2, bears some genetic mutations not seen in the original omicron lineage, and some of these mutations lie in the spike protein, according to the World Health Organization (opens in new tab) (WHO). Some preliminary data hint that BA.2 may be slightly more transmissible (opens in new tab), but not more severe, than the original omicron, but it's too early to interpret that data with any confidence.

In December, scientists reported that the original version of omicron had split into multiple sublineages, one of these being BA.2, Live Science previously reported. BA.2 bears a genetic quirk that makes it harder to track using PCR tests, so it's been nicknamed "stealth omicron." 

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The original omicron carries a "deletion" in the gene that codes for its spike protein, which the virus uses to infect cells. PCR tests for SARS-CoV-2 scan for several genes, including the spike protein gene, and when a variant carries this deletion, the PCR test displays an error that reads "S gene target failure." This error makes it easy to flag likely omicron cases and then run the samples through a full genomic analysis to confirm.

The BA.2 sublineage, however, does not carry this deletion, known as 69-70del, so it doesn't stand out on PCR tests from other variants that lack the deletion. A person with BA.2 will still test positive for the coronavirus on a PCR test, but their case won't be flagged as BA.2 unless their original sample goes through genetic sequencing.

"Don't get the impression that 'stealth omicron' means we can't detect it," Dr. S. Wesley Long, a pathologist at Houston Methodist in Texas, told The Associated Press (AP). 

So far, stealth omicron has been detected in 40 countries, including the U.S., according to the AP. In general, BA.2 currently appears more common in Asia and Europe than on other continents. 

The U.K. Health Security Agency has designated BA.2 as a "variant under investigation," in light of the country's rising number of BA.2 cases, although BA.1 remains dominant overall. In Denmark, the variant was responsible for 45% of COVID-19 cases in mid-January, up from 20% at the beginning of the month, the AP reported. And as of Monday (Jan. 24), BA.2 accounted for 65% of Denmark's new coronavirus cases, Anders Fomsgaard, a virologist at the State Serum Institute in Denmark, told The Washington Post (opens in new tab). Overall, coronavirus cases are still increasing in Denmark.

In the U.S., BA.2 does not make up a similarly high proportion of coronavirus cases as seen in the U.K. and Denmark, James Musser, director of the Center for Molecular and Translational Human Infectious Diseases Research at Houston Methodist, told The Washington Post. Houston Methodist recently identified three BA.2 cases, but as of now, the sublineage hasn't gained much ground in the U.S., Long told the AP. The mutant has also been spotted in Connecticut (opens in new tab) and California (opens in new tab), among other states, according to news reports.

In all, the U.S. has submitted 96 BA.2 genetic sequences to GISAID, a global platform for sharing coronavirus data, the AP reported. About 15,000 sequences have been submitted, globally. 

As BA.2 cases are increasing worldwide, the WHO now recommends that health agencies study how the sublineage compares with the original omicron, particularly in terms of its ability to spread and cause severe disease. 

"Investigations into the characteristics of BA. 2, including immune escape properties and virulence, should be prioritized independently (and comparatively) to BA. 1," the original version of omicron, the WHO website reads (opens in new tab).

"Currently, there are insufficient data to determine whether the BA.2 lineage is more transmissible or has a fitness advantage over the BA.1 lineage," Kristen Nordlund, a spokeswoman for the Centers for Disease Control and Prevention (CDC), told The Washington Post. "CDC continues to monitor variants that are circulating both domestically and internationally."

Early reports from Denmark suggest that the hospitalization rate for BA.2 does not differ from that of the primary omicron lineage, the AP reported. "We so far do not see major differences in age distribution, vaccination status, breakthrough infections and risk of hospitalization. Also, despite the high infection rate of BA. 2, the numbers of hospitalizations [in] ICUs are decreasing," Fomsgaard told The Washington Post.

There are some hints that the sublineage is as transmissible, or slightly more transmissible, than the original omicron, "but we don't necessarily know why that is," Long told the AP. And in laboratory studies, scientists are now testing whether antibodies against the original omicron also target and neutralize BA.2, the AP reported. 

The two versions of omicron are similar enough that there's a good chance that infection with omicron "will give you cross-protection against BA.2," Dr. Daniel Kuritzkes, an infectious diseases expert at Brigham and Women’s Hospital, told the AP.

Read more about stealth omicron in The Associated Press (opens in new tab) and The Washington Post (opens in new tab)

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.