CIDRI-Africa on high alert following detection of Omicron variant

28 Nov 2021
28 Nov 2021

The Wellcome Centre for Infectious Diseases Research in Africa (CIDRI- Africa) is on high alert following the recent observation of a rapid increase in spike gene target failure (SGTF) in SARS-CoV-2 diagnostic samples in Gauteng province, South Africa.  Preliminary data suggests that this SGTF is linked to a mutation in SARS-CoV-2 B1.1.529, a variant recently shown to be increasing in frequency in this province.  On 26th November 2021, WHO designated B1.1.529 a Variant of Concern (VOC), named Omicron.

We anticipate this variant has already spread across South Africa, as it has been circulating for some weeks in Gauteng province, which is the economic hub of the country.  Analysis of previously identified positive diagnostic samples for SGTF using the TaqPath Assay indicates that Omicron has indeed spread to the Western Cape province; 18 of 22 retrospectively tested samples from recent inpatients at Groote Schuur Hospital show SGTF.

CIDRI-Africa is increasing our sequencing and SGTF monitoring to track the spread of this VOC. We have systems in place to monitor any possible impact on disease severity.  Positive diagnostic samples are still low in number as the epidemic in the Western Cape lags that in Gauteng. 

Please visit the National Institute for Communicable Diseases and Network for Genomic Surveillance South Africa pages for more information on genomic surveillance of Omicron.