Omicron sub-lineage BA.2 designated as Variant Under Investigation

The Omicron variant sublineage known as BA.2 has been designated a Variant Under Investigation (VUI-22JAN-01) by the UK Health Security Agency (UKHSA).

Overall the original Omicron lineage, BA.1, is dominant in the UK and the proportion of BA.2 cases is currently low. The designation was made on the basis of increasing numbers 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.

To date there have been 426 cases of Omicron BA.2 confirmed by Whole Genome Sequencing in England, with the earliest dated 6 December 2021. The areas with the largest number of confirmed cases are London (146) and the South East (97). Data for the devolved administrations will follow in due course. 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.

40 countries have uploaded a total of 8,040 BA.2 sequences to GISAID since 17 November 2021. At this point it is not possible to determine where the sublineage 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).

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

Dr 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. So far there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1, but data is limited and UKHSA continues to investigate.

“Case rates remain high throughout the UK and we must remain vigilant and take up vaccinations. We should all continue to test regularly with LFDs and take a PCR test if symptoms develop”.

Health and Social Care Secretary, Sajid Javid, said:

“We are learning to live with this virus - and thanks to our world-leading surveillance system we can rapidly detect and carefully monitor any genetic changes to COVID-19.

“Our exceptional vaccine rollout means the number of people severely affected by COVID-19 is low, and the UK’s innovation and research has discovered life-saving treatments for those most at-risk from COVID-19.

“As we cautiously return to Plan A, I encourage you to give yourself and your loved ones the best protection possible and Get Boosted Now.”

As is routine for any new variants under investigation, UKHSA is carrying out laboratory and epidemiological investigations to better understand the characteristics of this variant. We will continue to monitor this situation closely and recommend appropriate public health measures if needed. More detail will be available in UKHSA’s regular Variant Technical Briefings.

UKHSA has published a new report on COVID-19 treatments

The UKHSA has now introduced a fortnightly technical briefing on the development and effectiveness of therapeutics used to treat patients with COVID-19 in the UK. Thanks to the success of the vaccination programme, the number of people in hospital or suffering from severe disease has been greatly reduced. There are a number of effective therapeutics in use in the UK to treat those who still encounter serious illness as a result of COVID-19.

The surveillance programme to support the roll out of novel therapeutics will examine the level of access to various treatments, the extent to which emerging mutations and variants may affect efficacy, and the ongoing picture of clinical outcomes. Updates will be published regularly.