UK designates Omicron sublineage BA.2 as a variant under investigation (VUI)

Jan. 28, 2022

The Omicron variant sublineage known as BA.2 has been designated as a variant under investigation (VUI-22JAN-01) by the UK Health Security Agency (UKHSA), according to an agency news release.

Overall, the original Omicron lineage, BA.1, is dominant in the United Kingdom (UK) and the proportion of BA.2 cases is currently low, the agency said. The original Omicron lineage also accounts for about 99.9% of cases in the United States, the Centers for Disease Control and Prevention (CDC), has said.

The UK Health Security Agency said the designation of VUI status for the new Omicron variant “was made based on the increasing number of of BA.2 sequences identified both domestically and internationally. There is still uncertainty around the significance of the changes to the viral genome, and further analyses will now be undertaken,” the agency said.  

To date, there have been 426 cases of Omicron BA.2 confirmed by whole genome sequencing (WGS) in the UK, with the earliest dated December 6, 2021.

The areas with the largest number of confirmed cases are London (146) and the Southeast (97).

The UKHSA also said that "early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed."

In total, 40 countries have uploaded 8,040 BA.2 sequences to GISAID since November 17, 2021. “At this point, it is not possible to determine where the sub-lineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark (6,411). Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127),” the UKHSA said.

Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously, the agency added.

Meera Chand, COVID-19 Incident Director at UKHSA, said, “It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge as the pandemic goes on. Our continued genomic surveillance allows us to detect them and assess whether they are significant.”

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