BA.2 Variant Raises Alerts Among Scientists Struggling To Track ‘Stealth’ Omicron

The number of COVID-19 cases fueled by the Omicron variant, known as BA.1, continues to rise. Scientists are struggling to track the “stealth” subvariant BA.2 as it overruns parts of Asia and Europe.

The BA.2 variant has been pegged as being 1.5 times more transmissible than the Omicron variant, but the two share similar genetic makeup and carry similar mutations.

“In many ways they are similar. Each have about 50 mutations. There are 30 mutations that are overlapping between these two viruses,” said Nevan Krogan, director of the Quantitative Biosciences Institute.

The differences found in the BA.2 variant is making it difficult for scientist to keep track of the strain. The Omicron variant lacks one of the three target genes on a PCR test, which means when the pattern appears, it is assumed to be the BA.1 infection.

However, BA.2 does not have the missing gene, forcing scientists to take a different route to track the subvariant.

“It does not have a mutation in a region that makes it drop out so it looks very much like Delta on a PCR test so you can’t tell the difference, and that is why we call it stealth,” said Dr. Deepak Srivastava, president of the Gladstone Institutes.

Similar to the Delta variant, researchers use the number of virus genomes on public databases to determine BA.2 cases.

Despite the more contagious strain, no evidence has been found that suggests the COVID-19 vaccine is ineffective against the BA.2 subvariant.

Trevor Bedford, a computational virologist at Fred Hutchinson Cancer Center, reported that as of Friday, BA.2 makes up roughly 82% of cases in Denmark, 9% in the U.K., and 8% of U.S. cases, based on data gathered from GISAID and the Our World in Data project at the University of Oxford.