‘Stealth’ Omicron is stealthy no more: What’s known about the BA.2 variant
As the Omicron coronavirus surge subsides, researchers are keeping an eye on a highly transmissible subvariant known as BA.2. Many epidemiologists suspect that it may reverse the decline of cases in the United States, but doubt that it will cause a large new spike.
Here’s what we know so far about BA.2.
It’s not really new. Scientists first discovered the Omicron variant in November, and it quickly became clear that the viral lineage already existed as three genetically distinct varieties. Each branch of Omicron had its own set of unique mutations.
At the time, the most common was BA.1, which quickly spread across the world. BA.1 was almost entirely responsible for the record-shattering spike in cases this winter. At first, BA.1 was a thousand times as common as BA.2. But in early 2022, BA. 2 started to be found in a larger proportion of new infections. It seems to be easier to catch.
Omicron created record-setting spikes of cases for two reasons: it was more transmissible than earlier variants, and it could evade some of the protection from vaccines and previous infections. But recently BA.2 has spread even faster than BA.1.
Scientists suspect that BA. 2’s rapid growth is thanks to its unique mutations. In the gene for the spike protein on the surface of the virus, BA.2 has eight mutations not found in BA.1. It appears that these mutations speed up BA.2 by making it more transmissible, rather than better able to evade immunity. In Denmark, for example, scientists found that people infected with BA.2 were substantially more likely to infect people they shared a house with than those with BA.1.
In England, researchers found that it took less time on average for someone with BA.2 to infect another person, accelerating its spread through communities. And in a
Places like Hong Kong that kept Covid out until now were not able to build up immunity through infections in previous waves. They also failed to vaccinate many citizens, particularly the elderly. Many who were vaccinated got relatively ineffective ones developed in China.
study in Hong Kong, researchers estimated that during an outbreak of BA.2 in a public housing complex, the virus doubled every 1.28 days.
It is not yet causing a new surge in the United States, and it’s not clear if it will.
By early 2022, BA.2 was growing more common in a number of countries. And by February, it had become dominant worldwide, driving down the once-dominant BA.1.
In some countries in Europe, the rise of BA.2 has roughly coincided with a halt in the decline of cases and a new surge. In Asia, places like Hong Kong that suffered little from earlier variants are now getting pummeled by BA.2.
It’s possible that BA. 2’s high transmissibility is driving these increases in cases. But it’s also hard to disentangle the subvariant’s effects from other factors.
Europe, for example, has just dropped many of its protection measures, making it easier for any coronavirus to jump from one person to another. People who got vaccinated early last year may be experiencing waning immunity, especially if they haven’t been boosted.
Places like Hong Kong that kept Covid out until now were not able to build up immunity through infections in previous waves. They also failed to vaccinate many citizens, particularly the elderly. Many who were vaccinated got relatively ineffective ones developed in China.
Existing vaccines work against the BA.2 variant.
One of Omicron’s most striking features was its ability to partly evade the protection of vaccines. “Breakthrough” infections became more common, helping to drive the case surge to its record high. But the vaccines continued to protect people against severe disease, espe
cially those who received a booster. Throughout the Omicron surge, vaccines remained highly effective against hospitalisations.
BA.2’s ‘stealth variant’ nickname is outdated.
BA.2 was nicknamed the “stealth variant” early in the Omicron wave, when scientists had a difficult time tracking it in positive PCR tests.
At the time, most infections were either caused by BA.1 or Delta. PCR tests use three genes to detect the coronavirus, and one of BA. 1’s mutations caused it to come up negative for one of those genes. That difference offered an easy way to track the variants: Delta would test positive for all three genes, whereas BA.1 would test positive for only two.
But BA.2 lacked the mutation that caused BA.1 to come up negative for one gene. That meant that when looking at PCR test results, BA.2 was indistinguishable from Delta — hence the “stealth variant” nickname.
But now that Delta has gone from dominant to rare, it’s easy to distinguish the two versions of Omicron on a PCR test. Viruses that test positive for only two genes are BA.1, and those that test positive on all three are BA.2.