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Two new sub-lineages of the Omicron variant have been detected in SA and some other countries. However, KRISP scientists say there is no cause for alarm at this stage. Known as BA.4 and BA.5, the team will continue to track their spread and study their properties. The detection of two new sub-lineages of the Omicron variant in South Africa serves as a reminder that the virus will continue to evolve and change over time.

'Continued evolution of the virus is entirely expected as it continues to circulate here in South Africa and around the world,' KRISP infectious diseases specialist, Dr Richard Lessells, told Health24.

The news of the sub-lineages, known as BA.4 and BA.5, became known after KRISP director, professor Tulio de Oliveira tweeted on Monday that they had been found in the country. However, he added that there was 'no cause for alarm' as SA has not seen any worrying increase in cases, hospitalisations, or deaths.

The good news is that BA.4 and BA.5 (like BA.1) can be identified by proxy marker of SGTF using the Thermo Fisher qPCR assay. These sublineages are responsible for an increasing share of sequenced cases in SA from early March and are well tracked by the NHLS and NGS-SA. pic.twitter.com/ng4B04k9Al

— Tulio de Oliveira (@Tuliodna) April 11, 2022

These sub-lineages have also been found in Botswana, Belgium, Germany, Denmark, and the UK, he said.

Lessells also said that while it was early days, scientists would continue tracking all the epidemiological indicators to assess the situation.

He added:

It’s important for people to be reassured that we continue to do all the work in the background to track all the different sub-lineages and to analyse them. But it shouldn’t be something that alarms the public.

Protection from vaccination and infection

De Oliveira explained in a Twitter thread that BA.4 and BA.5 share a similar spike profile with BA.2, the sub-lineage that is currently behind the majority of Covid cases globally, including SA. However, the newly detected sub-lineages also have additional mutations (changes to the virus's genes).

'[This] suggests to us that these sub-lineages may have a slightly different ability to get around some of our layers of immune protection, compared to BA.1 and BA.2,' Lessells said. 'But, again, they do not indicate a major shift that would suggest the virus can get around all the different layers of immune protection.'

It is expected that the immunity induced by vaccination or natural infection (or both) will offer good protection against severe disease, he said.

'What’s important is that people at high risk of severe disease (those over 50 years and people with chronic health conditions) make sure they are up-to-date with vaccination so that their protection is as strong as it can be,' added Lessells.

Slight differences, but no major impact on behaviour

BA.4 and BA.5 also differ from each other, in terms of amino acid mutations outside the spike protein, de Oliveira told Bloomberg.

Lessells explained: 'This just means that the BA.4 and BA.5 sub-lineages have the same mutations in the spike protein (the part of the virus we tend to be most interested in because mutations there can affect how well the virus infects cells, and how well it gets around some of our immune protection).