Omicron subvariants rise in prevalence as South Africa's positivity rate jumps overnight

Two Omicron subvariants are rising rapidly in South Africa and have increased in prevalence from 16% to 44%, according to the latest sequencing data released by the National Institute for Communicable Diseases on Monday.

South Africa’s positivity rate (the percentage of cases testing positive) jumped from 16% over the weekend to 19.3% on Monday, according to the latest statistics released by the NICD, with another 1,954 people testing positive for the virus. Sinehlanhla Jimoh from the NICD said 10,144 people tested for the virus on Monday.

The data in the sequencing report published on Monday analyses the results of sequencing tests to identify the variant of the SARS-CoV-2 virus in samples, where patients tested positive for infection, collected up to 22 April.

According to this report, the original version of Omicron – BA.1 – dominated the January data (55%), BA.2 dominated in February, March and April, but two additional sublineages of the Omicron variant (BA.4 and BA.5) increased in prevalence during March (16%) and appear to be increasing in April (44%) although additional sequencing data is needed for this period.

Another sublineage, BA.3, continues to be detected but only at low levels.

BA.4 and BA.5 have been designated sub-variants of interest by the World Health Organization, with no evidence yet of increased severity of symptoms or immune escape. In the latest sequencing report, scientists said while the mutations on these two sub-variants are not defined, it may be linked to an increased ability to escape the body’s immunity against SARS-CoV-2.

The authors of the report indicated that they are also monitoring data for recombinants. A recombinant of the Omicron and Delta variants was first identified and then designated as a variant of concern by the World Health Organization in January 2022. 

Jimoh said in the NICD’s daily update that the majority of new cases registered on Monday are from Gauteng (55%), followed by KwaZulu-Natal (23%). Western Cape accounted for 11%; Free State for 3%; Eastern Cape, Mpumalanga and North West each accounted for 2%, and Limpopo and Northern Cape each accounted for 1% of Monday’s new cases.

There have also been 65 new hospital admissions. A total of 2,282 people are currently being treated in hospital for Covid-19 related complications in South Africa. The fourth wave, driven by the “original” Omicron virus, was much milder than the previous three waves in the country.

In the last week of March, researchers who monitor the country’s wastewater systems for the presence of SARS-CoV-2 genetic material, raised the alarm that they were seeing an increase.

The CEO of the South African Medical Research Council, Prof Glenda Gray, at the time expressed concern over rising concentrations of SARS-CoV-2 RNA at certain wastewater treatment plants.

At the time, concentrations in wastewater samples from Cape Town and Nelson Mandela Bay were highlighted. 

Prof Angela Mathee, a member of the team monitoring the Western Cape’s wastewater, said at the time that their analyses also pointed to a sharp rise in SARS-CoV-2 concentrations in wastewater samples collected from sentinel towns in the Western Cape’s Breede Valley area, as well as an increase in concentrations at Cape Town International Airport. DM/MC