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‘Stealth’ variant no cause for alarm, but could slow case decline


A coronavirus drive-through testing site in Atlanta on Jan. 26, 2022. A new variant of the Omicron family could drag out the surge of cases around the world.

By Carl Zimmer


In recent days, headlines about a “stealth” omicron variant have conjured the notion that a villainous new form of the coronavirus is secretly creating a disastrous new wave of COVID-19.


That scenario is highly unlikely, scientists say. But the new variant, which goes by the scientific name BA.2 and is one of three branches of the omicron viral family, could drag out the omicron surge in much of the world.


So far, BA.2 doesn’t appear to cause more severe disease, and vaccines are just as effective against it as they are against other forms of omicron. But it does show signs of spreading more readily.


“This may mean higher peak infections in places that have yet to peak, and a slowdown in the downward trends in places that have already experienced peak omicron,” said Thomas Peacock, a virologist at Imperial College London.


In November 2021, researchers in South Africa first raised the alarm about omicron, which carried 53 mutations setting it apart from the initial coronavirus strain isolated in Wuhan, China. Some of those mutations enabled it to escape the antibodies produced by vaccines or previous infections. Other mutations appear to have made it concentrate in the upper airway, rather than in the lungs. Since then, omicron’s genetic changes have driven it to dominance across the world.


Within weeks of omicron’s emergence, however, researchers in South Africa started finding a few puzzling, omicronlike variants. The viruses shared some of omicron’s distinctive mutations but lacked others. They also carried some unique mutations of their own.


It soon became clear that omicron was made up of three distinct branches that split off from a common ancestor. Scientists named the branches BA.1, BA.2 and BA.3.


The earliest omicron samples belonged to BA.1. BA.2 was less common. BA.3, which was even rarer, appears to be the product of a kind of viral sex: BA.1 and BA.2 simultaneously infected the same person, and their genes were scrambled together to create a new viral hybrid.


At first, scientists focused their attention on BA.1 because its occurrence outnumbered the others by a ratio of 1,000 to 1. A lucky break made it easy for them to track it.


Common PCR tests typically detect three coronavirus genes. But the tests can identify only two of those genes in BA.1 because of a mutation in the third gene, known as spike.


In December, researchers in South Africa found that a growing number of PCR tests were failing to detect the spike gene — a sign that BA.1 was becoming more common. (The dominant variant at the time, known as delta, didn’t cause spike failures in PCR tests.) As omicron rose, delta waned.


Unlike BA.1., BA.2 lacks the spike mutation that makes PCR tests fail. Without the ability to use PCR tests to track BA.2, some scientists nicknamed it the “stealth” version of omicron.


But BA.2 wasn’t invisible: Researchers could still track it by analyzing the genetic sequences of samples from positive tests. And once delta virtually disappeared, scientists could use PCR tests to tell the difference between BA.1 and BA.2: Samples that caused spike failures contained BA.1, whereas the ones that didn’t contained BA.2.


In recent weeks, BA.2 has become more common in some countries. In Denmark, BA.2 makes up 65% of new cases, the Statens Serum Institut reported Thursday. So far, however, researchers there have found that people infected with BA.2 are no more or less likely to be hospitalized than those with BA.1.


On Friday, the British government released another early analysis of BA.2, finding that the variant makes up just a few percent of cases there. Still, surveys across England show that it is growing faster than BA.1 because it is more transmissible.


Reassuringly, the British researchers found that vaccines were just as effective against BA.2 as BA.1.


Trevor Bedford, a virus expert at the Fred Hutchinson Cancer Center in Seattle, found a similar pattern in the United States in viral sequences from recent test samples. He estimated that about 8% of cases in the U.S. are BA.2, and that figure is climbing fast, he added.


“I’m fairly certain that it will become dominant in the U.S.,” Nathan Grubaugh, an epidemiologist at the Yale University School of Public Health, said, “but I don’t yet know what that would mean for the pandemic.”


It’s conceivable that BA.2 could lead to a new surge, but Grubaugh thinks it’s more likely that COVID-19 cases will continue to decline in weeks to come. It’s also possible that BA.2 may create a small bump on the way down or simply slow the fall. Experiments on BA.1 now underway may help scientists sharpen their projections.

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