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A drive-through coronavirus testing site in Atlanta on Jan. 26, 2022. (Dustin Chambers/The New York Times)
In recent days, headlines about a ‘sneaky’ omicron variant have conjured up the notion that an evil new form of the coronavirus is secretly creating a disastrous new wave of COVID-19.
According to scientists, that scenario is quite unlikely. However, the new variant, which has the scientific name BA.2 and is one of three branches of the omicron viral family, could prolong the omicron wave in much of the world.
So far, BA.2 does not appear to cause more severe disease, and vaccines are as effective against it as they are against other forms of omicron. However, it does show signs of spreading more easily.
“This could imply higher spikes in infections in places that have not yet peaked and a slowing of downward trends in places that had already experienced a spike with the omicron variant,” said Thomas Peacock, a virologist at the University London Imperial.
In November 2021, researchers in South Africa were the first to sound the alarm about omicron, which had 53 mutations that set it apart from the initial strain of coronavirus isolated in Wuhan, China. Some of those mutations allowed it to escape antibodies produced by vaccines or previous infections. Other mutations appear to cause the variant to concentrate in the upper airway, rather than the lungs. Since then, genetic changes to the omicron have made it the dominant variant in the world.
However, within weeks of the appearance of omicron, researchers in South Africa began to find a few mysterious variants similar to it. The viruses shared some of the omicron’s distinctive mutations, but lacked others. They also had some mutations of their own that were unique.
It soon became apparent that the omicron was made up of three distinct branches stemming from a common ancestor. Scientists named the branches BA.1, BA.2, and BA.3.
The first samples of the omicron belonged to the BA.1. The BA.2 was less common. BA.3, which was even more unusual, appears to be the product of a kind of viral sex: BA.1 and BA.2 infected a person at the same time and their genes scrambled to create a new viral hybrid. .
At first, scientists focused their attention on BA.1 because its presence outnumbered the others by a ratio of 1,000 to 1. A hot streak made it easier for them to track it down.
Ordinary PCR tests usually detect three genes of the coronavirus. However, tests can only identify two of those genes in BA.1 due to a mutation in the third gene, known as the spike.
In December, researchers in South Africa found a growing number of PCR tests missing the spike gene, a sign that BA.1 was becoming more common (the dominant variant at the time, known as delta, did not cause failure of the spike in the PCR tests). As the presence of the omicron increased, that of the delta variant decreased.
Unlike BA.1, BA.2 does not have the spike mutation that causes errors in PCR tests. Because you can’t use PCR tests to track BA.2, some scientists have dubbed it the “stealth” version of the omicron.
However, BA.2 was not invisible: researchers could still track it down by analyzing the genetic sequences of positive test samples. And once the delta was almost gone, the scientists were able to use PCR testing to note the differences between BA.1 and BA.2: the samples that caused the spike failures contained BA.1, while those that didn’t. errors had BA.2.
In recent weeks, BA.2 has become more common in some countries. In Denmark, BA.2 accounts for 65 percent of new cases, the Statens Serum Institut reported Thursday. So far, however, researchers at that institute 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 nascent analysis of BA.2, finding that the variant accounts for only a small percentage of cases in that country. However, studies across England show that it is growing faster than BA.1 because it is more transmissible.
The most reassuring finding of the British researchers was that the vaccines are just as effective against BA.2 as BA.1.
From recent test samples, Trevor Bedford, a virus expert at the Fred Hutchinson Cancer Research Center in Seattle, found a similar pattern in viral sequences in the United States. Bedford estimated that about 8 percent of cases in the United States were BA.2, adding that number is rising fast.
“I’m pretty sure it’s going to be the dominant variant in the United States, but I don’t know what that will mean for the pandemic yet,” said Nathan Grubaugh, an epidemiologist at the Yale University School of Public Health.
It is conceivable that BA.2 could produce a new wave, but Grubaugh thinks it is more likely that COVID-19 cases will continue to decline in the weeks to come. It is also possible that BA.2 creates a small spike in the decline or simply slows the decline. Ongoing experiments on BA.1 could help scientists improve their projections.