The SA Medical Research Council (SAMRC) says its scientists have detected the Covid-19 Omicron variant in Cape Town and Nelson Mandela Bay.

The variant was detected in most wastewater treatment plants tested in Cape Town, and in a sample collected at Cape Town International Airport (CTIA).

The council has been monitoring the variant in four provinces.

“Individuals with Covid-19 are known to shed viral remains in their faeces. Though these fragments are not infectious, they can be detected in wastewater treatment plants and quantified to give an indication of likely Covid-19 cases. They can also be used to screen for variants using PCR methods and next-generation sequencing (NGS),” SAMRC Genomics Centre director Prof Craig Kinnear said.

The Omicron variant was found in 11 of 12 wastewater samples collected from Cape Town treatment plants on November 30.

“The Delta variant remained dominant in only one treatment plant,” SAMRC Biomedical Research and Innovation Platform deputy director Prof Rabia Johnson said.

“We have also detected Omicron in a series of wastewater samples collected from the Cape Town International Airport. Our data show Omicron was first detected at CTIA on November 23.”

The SAMRC said it had not yet determined the extent to which Omicron had spread to rural areas outside Cape Town. “However, genetic sequencing on a sample of wastewater collected from Rawsonville in the Breede Valley indicated the absence of Omicron, with the Delta variant remaining dominant.

“This does not necessarily mean Omicron is not being transmitted in these areas.”

The SAMRC also conducted tests in Nelson Mandela Bay in partnership with Nelson Mandela University. Preliminary results show three of four wastewater treatment plants in the city are positive for Omicron.

“Wastewater plays a crucial role in surveillance of SARS-CoV-2 as it can rapidly identify hotspots and circulating variants, in turn allowing for a rapid public health response.

“SAMRC-WSARP [Wastewater Surveillance and Research Programme] results generated this week show concentrations of SARS-CoV-2 fragments are increasing in almost all Cape Town wastewater treatment plants and other parts of the country.”

SAMRC president and CEO Prof Glenda Gray said it is crucial that everyone gets vaccinated and adheres to non-pharmaceutical interventions, such a wearing masks and social distancing.

“Essential gatherings should preferably be held outdoors or in well-ventilated indoor spaces to curb the transmission of Covid-19 during the festive season. We advocate for fellow South Africans to vaccinate before vacation,” she said.

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