SA scientists pore over new coronavirus sub-variants of omicron

SA scientists are scrutinising the rise of two new sub-variants of the highly transmissible omicron strain of coronavirus, to determine whether they are more infectious or dangerous than older lineages.

The prevalence of the sub-variants BA.4 and BA.5 has rapidly increased in SA in the past six weeks, rising from 10% to more than 40% of the Sars-CoV-2 genomes sequenced by local scientists, according to the National Institute of Communicable Diseases (NICD).

“We have learnt to be careful and we are watching very closely,” said Anne von Gottberg, a senior scientist at the NICD’s Centre for Respiratory Diseases and Meningitis.

Each of SA’s four coronavirus waves has been driven by a different variant, each more transmissible than the last.

However, at this stage there was no cause for alarm, as the increasing prevalence of BA.4 and BA.5 has not been matched by a surge in cases or hospital admissions, said Gottberg.

On Wednesday, 172 cases of BA4 and BA5 had been confirmed in SA with genomic sequencing, she said. This figure was “the tip of the iceberg” as SA only sequences about 1% of the positive samples identified by testing laboratories, she said. The World Health Organisation (WHO) recommends testing 5% of positive samples, and many European countries sequence a significantly higher proportion. The two sub-lineages had been identified in seven provinces, she said.

Scientists were concerned about some of the mutations on the spike protein in BA.4 and BA.5, which have the potential for increased transmissibility and better ability to evade antibodies generated by previous infection or vaccination.

Laboratory work is under way to gauge their capacity for immune escape, but results are not expected for several weeks.

The WHO said on Tuesday that BA.4 and BA.5 had also been detected in Botswana, the UK, Belgium, Denmark, and Germany. There was no evidence so far that there were any significant epidemiological differences between these two sub-lineages and their sister lineages BA.1, BA.2 and BA.3, it said. 

The WHO’s Africa regional head, Matshidiso Moeti, urged countries to enhance their genomic surveillance to detect potentially dangerous variants, and to submit their data to publicly available databases.

kahnt@businesslive.co.za