Omicron present in five out of nine South African provinces – data

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JOHANNESBURG — The Omicron variant of the coronavirus has been detected in five out of nine South African provinces and accounted for 74% of the virus genomes sequenced in November, data from the country’s National Institute for Communicable Diseases (NICD) showed on Wednesday.

The variant, which has raised global fears of a surge in infections, was first detected in southern Africa last week.

The NICD said the earliest detection of the variant in South Africa was on Nov. 8 in Gauteng, the most populous province. It said that until the end of October, the Delta variant accounted for most of the genomes sequenced, but in November Omicron had overtaken Delta.

Color-coded graphs showed that Omicron had now appeared in the provinces of Gauteng, Eastern Cape, KwaZulu Natal, Mpumalanga, and Western Cape.

The NICD did not give a total number of confirmed cases of Omicron infection. South Africa conducts genome sequencing on only a small proportion of total samples collected because of limited capacity, so the total number of cases could be much higher than the number of sequences reported.