‘Stealth’ Omicron Variant No Cause for Alarm, but Could Slow Case Decline

In recent days, headlines about a “stealth” variant of Omicron have raised the idea that a nasty new form of the coronavirus is secretly creating a disastrous new wave of Covid.

This scenario is highly unlikely, say the scientists. But the new variant, which bears the scientific name BA.2 and is one of three branches of the Omicron viral family, could lead to the surge of Omicron in much of the world.

So far, BA.2 does not appear to cause more severe disease and vaccines are just as effective against it as against other forms of Omicron. But it shows signs of spreading more easily.

“This may mean higher peaks of infections in places that have not yet peaked and slower downward trends in places that have already seen the Omicron peak,” said Thomas Peacock, virologist at Imperial College London.

In November 2021, researchers in South Africa first sounded the alarm about Omicron, which carried 53 mutations distinguishing it from the initial strain of coronavirus isolated in Wuhan. Some of these mutations have allowed it to evade antibodies produced by vaccines or previous infections. Other mutations appear to have caused it to concentrate in the upper respiratory tract rather than the lungs. Since then, Omicron’s genetic changes have led him to dominate the world.

However, within weeks of Omicron’s emergence, researchers in South Africa began to find some puzzling Omicron-like variants. The viruses shared some of Omicron’s distinctive mutations, but lacked others. They also carried their own unique mutations.

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

The first samples of Omicron belonged to BA.1. BA.2 was less common. BA.3, which was even rarer, appears to be the product of some kind of viral sex: BA.1 and BA.2 simultaneously infected the same person, and their genes were mixed 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 one. A lucky break made it easy for them to follow him.

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

In December, researchers in South Africa found that an increasing 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, did not cause peak failures in PCR tests.) As Omicron increased, Delta decreased.

Unlike BA.1., BA.2 does not have the spike mutation that causes PCR tests to fail. Without the ability to use PCR tests to track BA.2, some scientists have dubbed it the “stealth” version of Omicron.

But BA.2 was not invisible: researchers could still track it by analyzing the genetic sequences of samples from positive tests. And once Delta was all but gone, scientists were able to use PCR tests to tell the difference between BA.1 and BA.2: samples that caused spike failures contained BA.1, while those that did not. not BA.2.

In recent weeks, BA.2 has become more common in some countries. In Denmark, BA.2 accounts for 65% of new cases, the Statens Serum Institut reported on Thursday. So far, however, researchers 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 UK government released another early analysis of BA.2, finding that the variant accounts for just a few percent of cases there. Yet surveys across England show it grows faster than BA.1 because it is more transmissible.

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

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

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

It is conceivable that BA.2 could lead to a further surge, but Dr Grubaugh thinks it is more likely that Covid cases will continue to fall in the coming weeks. It is also possible that BA.2 creates a small bump on the way down or simply slows down the fall. Experiments on BA.1 currently underway could help scientists refine their projections.