Friday, January 21, 2022

UKHSA: Omicron Sublineage BA.2 Designated as A VUI (Variant Under Investigation)


Although we first looked at it's growing diversity in mid-December (see The Omicron Uncertainty Principle), the now dominant Omicron variant is actually comprised of four closely-related viral lineages; B.1.1.529, BA.1, BA.2 and BA.3.

While B.1.1.529 was the progenitor of the Omicron lineage, BA.1 has been, by far, the most commonly reported version (> 99%).

BA.3 remains the rarest of the four, but the BA.2 sublineage has in recent weeks begun to make a move in several scandinavian countries (Denmark, Norway, Sweden). 

Yesterday, in Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases  and in Norwegian Institute of Public Health Also Reports A Rapid Increase In Omicron BA.2 Subvariant) we looked at these reports. 

At this time, we have zero information on how BA.2 infection might differ from BA.1, assuming it does at all.  But there are concerns that BA.2 may prove even more transmissible. 

Today the UK's Health Security Agency (UKHSA) has taken notice of a low, but rising number, of BA.2 cases in the UK, and has designated BA.2 as a VUI.  

Unlike BA.1 - which has the SGTF (Spike Gene Target Failure) which helps identify it with certain PCR tests - BA.2 simply tests positive as COVID, and requires additional genomic sequencing to identify its lineage. 

This from the UKHSA.

Omicron sub-lineage BA.2 designated as a variant under investigation (VUI)

The Omicron variant sub-lineage 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 (WGS), 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.

In total, 40 countries have uploaded 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 (SGTF) 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.

While there is considerable consternation in the media, and on some social media sites, over this BA.2 lineage, it is still too early to know how much of an impact it will have on the pandemic.  It does remind us, however, that SARS-CoV-2 continues to evolve, and that more surprises may lay ahead.

Stay tuned.