Scientists on alert over rising cases caused by Omicron cousin

The highly transmissible Omicron variant of the SARS-CoV-2 virus – the most common form of which is known as BA.1 – now accounts for nearly all of the coronavirus infections globally, although dramatic surges in Covid cases have already peaked in some countries.

Scientists are now tracking a rise in cases caused by a close cousin known as BA.2, which is starting to outcompete BA.1 in parts of Europe and Asia. The following is what we know so far about the new subvariant:

“Stealth subvariant”

Globally, BA.1 accounted for 98.8% of sequenced cases submitted to the public virus tracking database GISAID as of Jan. 25. But several countries are reporting recent increases in the subvariant known as BA.2, according to the World Health Organization.

In addition to BA.1 and BA.2, the WHO lists two other subvariants under the Omicron umbrella: BA.1.1.529 and BA.3. All are closely related genetically, but each features mutations that could alter how they behave.

Trevor Bedford, a computational virologist at Fred Hutchinson Cancer Center who has been tracking the evolution of SARS-CoV-2, wrote on Twitter on Friday that BA.2 represents roughly 82% of cases in Denmark, 9% in the UK and 8% in the United States, based on his analysis of sequencing data from the GISAID database and case counts from the Our World in Data project at the University of Oxford.

The BA.1 version of Omicron has been somewhat easier to track than prior variants. That is because BA.1 is missing one of three target genes used in a common PCR test. Cases showing this pattern were assumed by default to be caused by BA.1.

BA.2, sometimes known as a “stealth” subvariant, does not have the same missing target gene. Instead, scientists are monitoring it the same way they have prior variants, including Delta, by tracking the number of virus genomes submitted to public databases such as GISAID.

As with other variants, an infection with BA.2 can be detected by coronavirus home tests kits, though they cannot indicate which variant is responsible, experts said.

More transmissible?

Some early reports indicate that BA.2 may be even more infectious than the already extremely contagious BA.1, but there is no evidence so far that it is more likely to evade vaccine protection.

Danish health officials estimate that BA.2 may be 1.5 times more transmissible than BA.1, based on preliminary data, though it likely does not cause more severe disease.

In England, a preliminary analysis of contact tracing from Dec. 27, 2021, through Jan. 11, 2022, by the UK Health Security Agency (HSA) suggests that household transmission is higher among contacts of people infected with BA.2 (13.4%) compared with other Omicron cases (10.3%).

The HSA found no evidence of a difference in vaccine effectiveness, according to the Jan. 28 report.

A critical question is whether people who were infected in the BA.1 wave will be protected from BA.2, said Dr. Egon Ozer, an infectious disease expert at Northwestern University Feinberg School of Medicine in Chicago.

That has been a concern in Denmark, where some places that saw high case counts of BA.1 infections were reporting rising cases of BA.2, Ozer said.

If prior BA.1 infection does not protect against BA.2, “this could be sort of a two-humped camel kind of wave,” Ozer said. “It’s too early to know if that will happen.”

The good news, he said, is that vaccines and boosters still “keep people out of the hospital and keep people from dying.”