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SAMRC: Rising levels of SARS-CoV-2 RNA fragments in Tshwane and NMB wastewater

The South African Medical Research Council (SAMRC) has confirmed rising concentrations of SARS-CoV-2 RNA fragments in wastewater in the cities of Tshwane (Gauteng) and Nelson Mandela Bay (Eastern Cape). This follows an earlier cautionary note from the SAMRC (issued on 19 November 2021) that their wastewater surveillance team had observed increasing volatility during the previous fortnight in the concentration of SARS-CoV-2 RNA fragments in wastewater samples.

In collaboration with laboratory partners, the SAMRC operates a Wastewater Research and Surveillance Programme through which more than 70 wastewater treatment plants across four provinces in the country are monitored on a weekly basis for the concentration of non-infectious RNA fragments of SARS-CoV-2, the virus causing COVID-19.

On Monday mornings, field staff collect samples from the wastewater treatment plants for delivery to partner analytical laboratories by midday, for extraction and analysis. By Wednesdays, after quality control checks, the findings are relayed to relevant municipal and other stakeholders.

Dr Rabia Johnson, Deputy Director of the SAMRC’s Biomedical Research & Innovation Platform (BRIP) and one of the scientists involved in the Programme, indicated that from the start to the end of November 2021, the picture had changed dramatically. “At the beginning of the month levels of SARS-CoV-2 RNA fragments in wastewater were mostly low or undetectable; now we’re measuring concentrations last seen during the third COVID-19 wave,” said Johnson.

Also working on the Programme, Dr Renée Street, who is the Deputy Director in the SAMRC Environment and Health Research Unit, described how the latest findings had been made possible through partnerships with the Sefako Makgatho Health Sciences and Nelson Mandela universities. She pointed out that the rising SARS-CoV-2 RNA concentrations are now evident in the majority of wastewater treatment plants in Tshwane. In addition, there is increasing volatility in SARS-CoV-2 RNA concentrations at wastewater treatment plants where levels had previously been low.

“Apart from the sharp increases in SARS-CoV-2 fragment concentrations being observed in community-based wastewater treatment plants, we are also picking up rising concentrations in wastewater samples collected from Cape Town International Airport,” she said.

According to Prof Glenda Gray, SAMRC President and CEO, the rapidly increasing concentrations of SARS-CoV-2 RNA fragments in wastewater are a major cause for concern, especially alongside reports of increases in COVID-19 cases and deaths in the past week. “Collectively, the evidence makes a compelling case for those who qualify for booster shots to get them urgently,” said Gray. She added that while the country has seen encouraging vaccination coverage, with more than 24m people having received at least one dose – and more than 15m fully vaccinated, the severity of this next wave will depend on whether the country achieves its vaccination targets.

Gray also urged healthcare workers who qualify for the booster shot to do so without delay by taking part in the Sisonke 2 Study – this, she said, was necessary to protect themselves against COVID-19 infections and admissions during the fourth wave which has already started.

On the new Omicron variant, scientists from the SAMRC Wastewater Surveillance Programme said although not much is known about it at this stage, they will monitor it as they have done with the other variants such as Delta. “With new and probably more contagious COVID-19 variants emerging locally and elsewhere, there is an increased need to monitor them and their presence in our communities to provide an early warning system for public health authorities.”


SAMRC article – AMRC confirms rapidly rising concentrations of SARS-CoV-2 RNA fragments in wastewater in Nelson Mandela Bay and Tshwane (Open access)


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