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Explainer: What is ‘stealth Omicron’ and should SF be concerned?

a woman in a mask swabs a mans nose
Source: Camille Cohen/The Standard

Just as local Covid case counts continue to decline from record numbers seen earlier this month and San Francisco announces relaxed indoor mask orders for fully vaccinated residents, reports have emerged of a new strain of the virus dubbed “Stealth Omicron.” 

After nearly two years and myriad new variants (remember Lambda?) it can be difficult to parse out what’s happening. Here’s what you need to know about the new Covid subvariant.  

So what exactly is Stealth Omicron?

The variation of the Covid virus is scientifically known as the BA. 2 subvariant, essentially a genetic sibling to the main Omicron variant, known as BA. 1. But the “stealth” title of the virus may be a bit of a misnomer, said Dr. John Swartzberg, an infectious disease expert at UC Berkeley. PCR tests have a more difficult time identifying the stealth strain as Omicron because of its particular genetic makeup. However, the tests still pick up whether an individual is infected by the virus. 

Why can’t tests identify the stealth strain in the same way?

PCR tests detect the presence of three specific parts of the virus’ genome. For the main Omicron strain, one of those target genes is not detected: a phenomenon called the S gene dropout, which makes it easier to identify a particular sample as Omicron. But with BA. 2, all three target genes are detected, meaning that identifying a particular case as Omicron generally requires whole genome sequencing. Still, with around 99% of the positive samples in the United States being the original Omicron variant, chances are a positive result means infection with the strain. 

What’s the difference between the new subtype and “original” Omicron?

Preliminary research shows that the new subtype could be twice as transmissible as the original Omicron strain, which is around three times more infectious than Delta, Swartzberg said. However, it is important to note that there is no evidence to show the new subvariant is more virulent— or likely to cause serious illness or death—than primary Omicron. “It’s reasonable to expect that it’s not going to have a major impact beyond the tremendous impact that Omicron has had, because if you had Omicron, you're likely going to have—at least for a short while—immunity toward getting to getting Omicron again,” Swartzberg said. 

How widespread is Stealth Omicron?

At least in the Bay Area, very few cases of the subvariant have been confirmed. According to the California Department of Public Health, around a dozen cases of the subvariant have been detected in the state, with two cases in Santa Clara County. The subvariant has become the dominant strain in Denmark and spread to European countries like the U.K. and Norway, and as far away as Hong Kong. 

Are my current vaccines or boosters effective?

If you are up to date with the vaccines and a booster shot, Swartzberg said, you likely have good protection from serious illness regardless of the specific strain of Omicron. 

Kevin Truong can be reached at