Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic

 The first sequenced omicron case was reported from Botswana on Nov 11, 2021, and a few days later another sequenced case was reported from Hong Kong in a traveller from South Africa.

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Several sequences from South Africa followed, after initial identification that the new variant was associated with an S-gene target failure on a specific PCR assay because of a 69–70del deletion, similar to that observed with the alpha variant.

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 The earliest known case of omicron in South Africa was a patient diagnosed with COVID-19 on Nov 9, 2021, although it is probable that there were unidentified cases in several countries across the world before then. In South Africa, the mean number of 280 COVID-19 cases per day in the week before the detection of omicron increased to 800 cases per day in the following week, partly attributed to increased surveillance.

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 COVID-19 cases are increasing rapidly in the Gauteng province of South Africa; the early doubling time in the fourth wave is higher than that of the previous three waves