COVID-19 Delta variant detected by SAMRC Wastewater Surveillance & Research Programme

Cape Town | Scientists from the South African Medical Research Council (SAMRC) have detected the presence of the highly infectious SARS-CoV-2 Delta variant in wastewater from several towns in the Western Cape, as well as the City of Cape Town, using their wastewater-based early warning system for COVID-19.  

The SAMRC established the Wastewater Surveillance & Research Programme (SAMRC-WSARP) in July 2020 as an extension of several interventions to support the country’s efforts to manage the COVID-19 pandemic. The Programme includes a SARS-CoV-2 Wastewater Surveillance Dashboard, an interactive public-facing dashboard to share information on levels of SARS-CoV-2 in wastewater in participating communities.

Wastewater-based surveillance for detecting SARS-CoV-2 has been carried out in a number of countries, and a good correlation has been found between viral load in wastewater and subsequent COVID-19 cases.

“For the past two months, SAMRC scientists have been screening for  the presence of mutations associated with the Alpha and Beta variants in wastewater using qRT-PCR technology, and found both the Alpha and Beta variants, with the Beta variant being predominant,” said Dr Rabia Johnson, Deputy Director of the SAMRC’s Biomedical Research & Innovation Platform (BRIP). “This week, however, the team acquired the reagents to also test for the Delta variant, and detected it as the dominant variant in towns in the Breede Valley (Worcester, Rawsonville, Touws River and De Doorns), Theewaterskloof (Bot River and Villiersdorp) as well as in 19 wastewater treatment plants in the Cape Town Metropole,” she added. This coincides with an increase of SARS-CoV-2 viral loads detected at these wastewater treatment plants, which according to the team’s knowledge, is the first time that scientists have been able to adapt this rapid and cost effective qRT-PCR method for mutation profiling of the SARS-CoV-2 delta variant in wastewater in South Africa.


The team of scientists also highlighted that although it is not yet known whether heavily trafficked routes play a role in COVID-19 transmission, several of the towns where the Delta variant has been found fall along one of the biggest national roads in the country.

According to the team, during the past few weeks, they have seen sharp increases in the levels of SARS-CoV-2 viral loads in most of the wastewater treatment plants, monitored by the SAMRC Wastewater Surveillance and Research Programme. According to Dr Mongezi Mdhluli, Chief Research Operations Officer at the SAMRC, “The Delta variant is highly contagious and in light of the findings from the SAMRC Wastewater Surveillance Programme, and their implications, we implore all in South Africa to adopt the highest level of precaution possible to disrupt transmission of COVID-19”.

Dr Johnson emphasized that data obtained from wastewater testing provides an overview of infections within communities served by specific wastewater catchment areas.  Wastewater is proving to be a valuable source of information for COVID-19 decision-making, particularly during the third wave.  “We hope to make testing for a range of SARS-CoV-2 variants a standard component of our weekly wastewater surveillance programme,” added Dr Johnson.

Drs Mary-Ann Davies and Natacha Berkowitz from the health departments of the Western Cape and City of Cape Town, respectively, expressed their concern over the widespread detection of the Delta variant in wastewater systems in the province and city, warning that the public health implications and burden on health services in the coming weeks was a major concern. They echoed calls for heightened public vigilance regarding non-pharmaceutical interventions which include the wearing of masks, social distancing, avoidance of gatherings and stringent hand hygiene.

SAMRC President and CEO, Professor Glenda Gray described this revelation as an encouraging step in mitigating the third wave in which the Delta variant is responsible for most of its infections. “The emergence of new and more contagious COVID-19 strains globally and especially in South Africa has increased the need to keep track of variants and their presence in communities,” said Gray, adding that tracking of these variants in wastewater could provide an early warning system for public health authorities.


Further information on the SAMRC Wastewater Surveillance Programme may be obtained on their Dashboard at

Release date: 
Tuesday, July 6, 2021 - 10:31
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