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New "Stealth" Omicron Sibling Could Make Tracking COVID Variant Harder


Dr. Katie Spalding

Katie has a PhD in maths, specializing in the intersection of dynamical systems and number theory.

Freelance Writer


Omicron? Never 'eard of 'im. Image credit: stockwars/UMBE/, edited by IFLScience

Can you hear the pitter-patter of tiny viruses? The Omicron variant just got a little sister.

Evolution happens at a breakneck speed when you’re a piece of genetic code coated in a protein layer, and it hasn’t taken long for Omicron to outsmart one of the only advantages we had on it. A newly-discovered sibling lineage of the COVID variant – known informally as “stealth Omicron” due to its ability to partially evade the PCR tests that can locate its brother so easily – has prompted researchers to split the strain in two.


“There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically,” Professor Francois Balloux, director of the University College London Genetics Institute, told The Guardian. “The two lineages may behave differently.”

When the Omicron variant was originally discovered at the end of last month, researchers noticed that it was missing one of the three gene markers – the S gene, specifically – used by commercial coronavirus test kits. That was a small ray of hope in what otherwise looked like a very calamitous situation: “We can detect [Omicron] very quick,” Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation in South Africa, explained at the time, “and this will help us to track and understand the spread.”

But the new offshoot, BA.2, no longer has this missing S gene, making it harder to track and impossible to identify with a simple PCR test.

Don’t panic though: “You can still detect it by PCR,” said Rob Knight, head of a genetic-computation lab at the University of California, San Diego, speaking to The Daily Beast. The new “stealth” lineage hasn’t rendered the tests useless – they’ll still pick up the infection, Knight explained, they just “can’t tell it apart from the dominant Delta strain.”


While it’s still possible to identify BA.2, it now requires detailed genetic sequencing rather than a quick and easy test – and that could slow down our ability to track the new lineage. The new baby Omicron has only been identified in seven cases so far, but “since [BA.2 is] not picked up by [PCR tests], there may be more Omicron than we think,” evolutionary geneticist Emma Hodcroft told the Financial Times.

Nevertheless, experts say we shouldn’t be too concerned just yet. The new lineage’s ability to escape being pinned down by PCR tests “can matter when we’re dealing with hundreds of cases,” Hodcroft said, “[but] from the numbers we have right now, I don’t think there’s a very large hidden burden from BA.2.”

University of Washington virologist Keith Jerome, whose lab was the first to detect Omicron cases in Washington state, agrees. Speaking to The Daily Beast, Jerome said he wasn’t all that worried about the new lineage: the sibling variant “could hide for a day or two,” he said, but “but if it becomes common at all we’ll find it via the random sequencing.”

While Omicron’s stealthy sibling may be cause for concern in countries that lack ready access to genome sequencing to monitor the spread, structural biologist David Stuart told the Financial Times that he doesn’t see “any reason to think that the new outlier is any more of a threat than the form of Omicron that’s knocking around at the moment.” And with the recent announcement from Pfizer that Omicron can be effectively neutralized by a triple vaccine dose, the advice for the general public hasn’t changed.


“I know everyone is ‘excited’ about Omicron,” Stephanie James, the head of a COVID testing lab at Regis University in Colorado, told The Daily Beast. “But variants are expected by the scientific community. The advice is the same – get vaccinated and wear a mask.”


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