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Omicron detected in City’s wastewater

Omicron detected in wastewater in the City. file

Omicron detected in wastewater in the City. file

Published Dec 11, 2021


Cape Town - The Omicron variant has been found in the City’s wastewater.

Scientists from the South African Medical Research Council (SAMRC) have detected the variant in wastewater samples collected in the City of Cape Town and the Nelson Mandela Bay.

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They said 92% of the samples taken showed the presence of Omicron.

Director of the SAMRC’s Genomics Centre Craig Kinnear said those with Covid-19 are known to shed the viral remains in their faeces.

“Although these fragments are not infectious, they can be detected in wastewater treatment plants and quantified to give an indication of likely Covid-19 cases locally. They can also be used to screen for circulating variants using PCR methods, as well as next-generation sequencing,” he said.

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Deputy director of the SAMRC’s Biomedical Research and Innovation Platform, professor Rabia Johnson, said a SARS-CoV-2 virus RNA in wastewater monitoring system had been in place since last year July.

“We found the Omicron variant in 11 of 12 samples of wastewater collected from Cape Town treatment plants on November 30. The Delta variant remained dominant in only one wastewater treatment plant tested.

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

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“The extent to which the Omicron variant has spread to rural areas outside the City of Cape Town is not known; however, genetic sequencing undertaken on a sample of wastewater collected from the rural town of Rawsonville in the Breede Valley (Western Cape) indicated the absence of Omicron, with the Delta variant remaining dominant,” said Johnson.

The SAMRC said the detection via wastewater was important as it identified the hotspot areas and allowed for a rapid response from the health sector.

As number of those testing positive continued to rise, Health Minister Joe Phaahla said there has been an increase in the hospitalisation of babies, toddlers and pregnant women.

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The Western Cape has had close to 500 positive cases of children, 40 of whom were admitted to hospital since last month.

The private health sector had also confirmed they are seeing a very different wave in the Western Cape, with children filling their beds at hospitals.

The provincial Education Department confirmed they have 29 active cases of Covid-19 at schools.

Clinical microbiologist, Professor Anne Von Gottberg said last week cases involving children showed uncomplicated clinical courses inside hospitals.

The World Health Organization confirmed Africa accounted for 46% of the nearly 1 000 cases of Omicron reported in 57 countries worldwide.

Immunization and Vaccines Development Programme co-ordinator for the WHO Regional Office for Africa, Dr Richard Mihigo, said only 6.3% of patients were admitted to ICU in South Africa compared to the huge influx of people in July during the Delta variant.

“So far, 10 African countries have reported cases. Despite the widespread global presence of Omicron, more than 70 countries have imposed travel bans that are mainly targeting southern African countries – some of which have yet to report any Omicron case,” he said.

Provincial Health spokesperson Mark van der Heever said compulsory tests for procedures enabled the detection of positive cases in children.

“Since the increase in cases in early November there have been 486 diagnosed cases in children of whom 40 have been admitted.

“Further investigation is needed to assess what proportion of the admissions with SARS-COV-2 in children are due to Covid-19 illness and what proportion are Covid 19 diagnoses in children admitted for other reasons such as surgery or other illness,” said Van der Heever.

Kerry Mauchline, of the Western Cape Education Department, said there were active cases involving children but could not confirm whether it was Omicron.

“This is an increase in cases compared to the past few weeks, and was expected given the resurgence of the pandemic in the province,” said Mauchline.

Chief clinical officer of Mediclinic Southern Africa Dr Gerrit de Villiers said their data also showcased an increase in younger patients.

“The patient profile for this wave includes younger patients and children under 12 years, which is significant in comparison to the previous three waves.

“These younger patients are overall not critically ill. We are also noting a number of asymptomatic patients, who were identified through testing on admission for other non-related procedures,” he said.

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