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Gauteng reports 10 cases of Omicron sublineage XAY

A cluster of 10 COVID-19 infections found in Gauteng has been linked to the XAY sublineage of the Omicron variant, according to the latest genomic sequencing report published by the National Institute for Communicable Diseases.

This specific sublineage was first identified in South Africa in July, and one case was found in Mpumalanga in August: the samples had “novel mutational profiles” as identified by scientists doing the sequencing.

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

Professor Anne von Gottberg from the NICD said the number of cases caused by these sublineages was so low it was not possible to say anything about their severity. Additionally, hospital admissions were not increasing, she added.

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. However, a variant 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.

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

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: 57 per 100 000 people, and lowest in Limpopo, at seven 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 Organisation’s weekly briefing on the pandemic, Dr Maria van Kerkhove said Omicron remained the dominant variant worldwide, and that they were tracking 200 sublineages of Omicron. “This virus continues to circulate at an incredibly intense level,” she said.

“Our ability to track variants and subvariants 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 up surveillance activities.”

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Daily Maverick article – Ten cases of Omicron sublineage found in Gauteng (Open access)


See more from MedicalBrief archives:


Omicron sub-variant BA.2 warning for US as European cases surge


NICD analysis finds Omicron subvariant increases risk of reinfection


COVID sub-variant spreads and new symptoms emerge




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