A cluster of 10 Covid-19 infections found in Gauteng has been linked to the XAY sublineage of the Omicron variant.

This is according to the latest genomic sequencing report published by the National Institute for Communicable Diseases on Friday.

This specific sublineage was first identified in South Africa in July, and one case was found in Mpumalanga in August.

The report said these were the samples that had “novel mutational profiles” as identified by scientists doing the sequencing.

According to the latest sequencing report, data up to August was assessed for all provinces with the exception of the North West. Only Gauteng and the Western Cape had September data available.

In general, scientists doing the sequencing found that Omicron remained the most prevalent of the variants in circulation, with Omicron BA.5 being the dominant subvariant. 

Prof Anne von Gottberg from the NICD said the number of cases caused by these sublineages was so low that it was not possible to say anything about their severity.

“We do know that admissions to hospitals are not increasing,” she said.

The American Centres for Disease Control explains a lineage as a group of virus variants that are closely related and derived from a common ancestor. A variant, on the other hand, has one or more mutations that differentiate it from other variants of the SARS-CoV-2 viruses. A recombinant is a variant created by a combination of genetic material from two different variants.

Omicron has been classified as a variant of concern by the World Health Organisation.

The latest epidemiological report issued by the NICD states that in the past week, 1,619 new cases were reported. This represents a 6.25% decline in case numbers.

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But, according to the latest report on testing for Covid in South Africa, the number of people testing had dropped by about 13% since last week.

The PCR testing rate was highest in Gauteng, at 57 per 100,000 people, and lowest in Limpopo, at 7 per 100,000.

The country saw a half-percent increase in positive cases since last week, with the highest test positivity rate recorded in Limpopo (8.3%), followed by Gauteng (8.0%), North West (7.9%) and Free State (5.6%). 

At last week’s World Health Organization’s weekly briefing on the pandemic, Dr Maria van Kerkhove said Omicron remained the dominant variant worldwide, and added that they were tracking 200 sublineages of Omicron. 

“The point being is that this virus continues to circulate at an incredibly intense level around the world. You heard the Director-General say today that the pandemic is not over, but that we see a light at the end of the tunnel.

“Part of ending this pandemic is really trying to reduce the spread of transmission, and there are simple measures that we can take to reduce the spread, while we also focus on preventing severe disease and death… but the more this virus circulates, the more opportunities it has to change, and this is something we are deeply concerned about,” she said.

“Our ability to track variants and subvariants around the world is diminishing because surveillance is declining and, with surveillance declining, the numbers of tests are declining, the number of sequences that are being conducted and being shared is declining… and that limits our ability to assess the known variants and subvariants, the ones that I have just mentioned, but also our ability to track and to identify new ones.

“This is why it’s really important that we keep surveillance activities up,” Van Kerkhove said. DM/MC