Omicron subvariant BA.2 raises new questions about puzzling evolution of virus behind COVID-19

Unlocking the mysteries behind Omicron's unique set of mutations will be key to understanding how this virus evolves and spreads — particularly as a tougher-to-detect subvariant is taking off in various countries, threatening to prolong this wave of infections.

The subvariant is known as BA.2 in the classification system used to catalogue mutations of SARS-CoV-2, and it's just one of a handful of Omicron subvariants featuring different mutations, which also includes the original lineage, BA.1, as well as BA.1.1, and BA.3.

BA.2 drew the close attention of virologists once it started to tick upward in multiple countries, including early signals of a slight rise here in Canada, suggesting it may be even more transmissible than its predecessor. 

"There is a competition," said Nathalie Grandvaux, a researcher and professor in the department of biochemistry and molecular medicine at the Université de Montréal. "It looks a bit like Delta versus Alpha … does that mean we will have another wave? It's not something we can say for now."

Denmark in particular is reporting a surge of BA.2 infections, with the subvariant accounting for nearly half of all Omicron cases by the second week of January, up from roughly 20 per cent over the end of 2021. 

"During the same period, the relative frequency of BA.1 has dropped," the Statens Serum Institut (SSI), a Danish research agency, reported on Jan. 20.

The U.K. is also monitoring BA.2 closely, and officials noted in a mid-January technical briefing that this subvariant is often able to fly under the radar. While BA.1 lacks one of the three target genes used in widespread SARS-CoV-2 testing, making it easy to spot — a process known as S-gene target failure — BA.2 can't be detected the same way.

The same report noted that by Jan. 1, BA.2 accounted for five per cent of the U.K.'s S-gene positive tests — and that figure keeps rising. 

That means the quick S-gene failure method to catch Omicron infections "is no longer sufficient to assess the spread of Omicron as a whole," it continued.

By contrast, for much of the pandemic's first year, it was far easier to track and manage this virus's evolution. 

That first changed when the B117 variant — later dubbed Alpha by the World Health Organization — burst onto the scene in late 2020, driving up case counts thanks to a set of mutations that helped it spread rapidly around the world.

As case counts ballooned, that evolutionary process has seemingly gone into overdrive, prompting variant after variant.

Strikingly, the differences between BA.1 and BA.2 are even greater than the differences between the original strain of SARS-CoV-2 and the Alpha variant, noted Denmark's SSI.

On Monday, the World Health Organization said research into how BA.2 operates should be "prioritized independently" from other Omicron subvariants.