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Wastewater testing shows signs that Covid-19 fifth wave looms

Wastewater testing shows signs that Covid-19 fifth wave looms
Jay Bhagwan
By Jay Bhagwan
25 Apr 2022
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Wastewater samples are showing signs of sustained higher levels of SARS-CoV-2 in Gauteng, KwaZulu-Natal, the Free State and the Western Cape.

In Gauteng, ongoing increases have been observed in wastewater at Rooiwal and Sandspruit (Tshwane North), Vlakplaats (Ekurhuleni South) and JP Marais (Ekurhuleni North), while stable higher levels have been observed at Daspoort (Tshwane South), Hartbeesfontein (Ekurhuleni North) and Goudkoppies (Johannesburg South).

Sustained increases were observed in eThekwini (Northern and Central) and in the City of Cape Town (Borcherds Quarry and Zandvliet). This is a sign of a looming next wave – the fifth – on the near horizon, as reported in Daily Maverick 168.

https://www.dailymaverick.co.za/article/2022-04-24-expert-sounds-alarm-on-fifth-wave-after-covid-19-curve-turns-upwards-in-sa/

The National Wastewater Based Surveillance programme is also examining SARS-CoV-2 genomics in wastewater and the sequencing data available up to week 12 show the presence of the Omicron variant in all recent samples across South Africa, with evidence of the new Omicron subvariant BA.4 present in southwestern Johannesburg. While some mutations associated with the Delta variant were also present, their significance remains unclear.

Based on this data and information, we are encouraging citizens to get vaccinated and to take more precautions by maintaining physical distancing, disinfection and wearing masks.

https://www.dailymaverick.co.za/article/2022-04-25-omicron-subvariants-rise-in-prevalence-as-south-africas-positivity-rate-jumps-overnight/

How it works


The concept of screening municipal wastewater and environmental water quality as an epidemiological tool for viruses is not new and is used to help inform broader infectious disease control efforts, such as the Global Polio Eradication Initiative. The South African science community continues its work under the umbrella of the South African Collaborative Covid-19 Surveillance System (Saccess).

Environmental surveillance is also used and recommended for other infections such as typhoid, as an early warning for hepatitis A and norovirus outbreaks, and for antimicrobial resistance, with modelling techniques used in the design and interpretation of those efforts.

Wastewater-based surveillance deals with a remnant nucleic acid particle of the SARS-CoV-2 virus and not a live virus, which means the procedure is safe. The detection of SARS-CoV-2 in sewage does not pose a risk of disease spread, but has the potential to determine the presence of infected individuals in a community.

SARS-CoV-2 RNA screening in raw sewage water using Rt-PCR can therefore be used to measure the virus circulation in a defined population, such as a city or a smaller municipality feeding into the same wastewater treatment works.

The Water Research Commission (WRC) continues to lead and fund this national initiative in partnership with the South African Local Government Association (Salga), which is coordinated and managed by the National Institute for Communicable Diseases (NICD) through a network of laboratories and several partnerships. The main aim of the programme is to share knowledge, stimulate research and innovation on water quality, sanitation and health in support of the government’s initiatives aimed at managing and curbing the spread of SARS-CoV-2. The programme consists of planned, interrelated activities aimed at achieving the objectives, by producing specified outputs. The aims and objectives are being achieved through:

  • Full-scale implementation of wastewater surveillance as a non-invasive approach for monitoring the spread of SARS-CoV-2 in communities;

  • Research and capacity building on SARS-CoV-2 in relation to water, sanitation and health; and

  • Knowledge dissemination through webinars and workshops.


The initiative has been sampling many of the sentinel strategic wastewater plants in key hotspot municipalities, covering nearly 120 plants across provinces – in metros, cities and rural towns – since its inception in early 2020. As resources become available, more wastewater treatment plants are being added to the surveillance network.

In addition, the initiative is complementing the many other initiatives by the government and municipalities. The programme is passionately driven and coordinated by a team at the NICD who produce weekly reports on the test samples.

As we progress, we have added the component of genomics to keep monitoring variants and their changes. All of this effort is to provide early warning and understand trends in the behaviour of this virus in our society. 

To support the sector, the initiative partners are happy to announce the launch by the NICD of an online dashboard to communicate wastewater results to stakeholders, including the public and policy-makers. It is freely available and may be configured to present both laboratory-confirmed cases and wastewater levels in specific geographical areas or wastewater treatment plants. More detailed information can be found here. DM

Jay Bhagwan is the Executive Manager of the Water Use, Wastewater Resources and Sanitation Futures Key Strategic Area at the Water Research Commission and led the WRC/Salga/NICD/Saccess National Wastewater Based Surveillance programme of the SARS-CoV-2 virus. The work of the NICD and the Saccess teams is acknowledged.

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