The Water Research Commission (WRC) has launched a National Programme on Monitoring Covid-19 Spread in Communities to track the prevalence of the virus in communities through wastewater surveillance and monitoring.

The WRC aims to work with local and international partners to research and measure the scope of the Covid-19 outbreak, independent from patient testing, across South Africa by testing wastewater samples in communities for the genetic fingerprint of the virus.

“Developing countries may not be able to afford or implement mass screening programmes to uncover new infections; however, there is an opportunity [to trace the] Covid-19 spread in sewered wastewater treatment systems and non-sewered sanitation systems that promises to provide us with information that could track and trace and signal hot spots of community transmissions,” says WRC research and development group executive Dr Stanley Liphadzi.

The SARS-CoV-2 genome is detected in faeces within the wastewater and sanitation environment, with studies showing it may survive in stools for three to four days. No infective strain has been confirmed as yet.

There is an opportunity to launch a wastewater surveillance project at a much lower cost and investment and larger reach to provide community-level indicators of South Africa’s position with regard to Covid-19 using a water- and sanitation-based approach, adds WRC CEO Dhesigen Naidoo.

The programme will use the best science and innovation processes in developing tools and techniques to successfully run a Covid-19 surveillance programme for the country, generating real-time data linked to geographic information system (GIS) mapping systems as an early warning system to deal with the current and next wave of Covid-19 in communities.

This aims to complement government’s Covid-19 initiatives by using the much broader environmental health surveillance initiative in order to establish a South African – and then African – chapter of the various programmes initiated worldwide.

Currently, countries such as Canada, Australia and the US, as well as many across Europe, are surveilling sewer systems to detect the virus’s fingerprint and provide indications of when the virus arrived, or as an early detection signal for communities that have already experienced an outbreak and are concerned about a resurgence.

While the developed world’s focus is on the safety of water services personnel and using this virus as a marker to determine the prevalence and health of their residents, for a developing country like South Africa, understanding the fate of the virus in water is of significance, as many communities in rural, dense and informal settlements are highly vulnerable, the WRC says.

The Covid-19 surveillance data from wastewater and sanitation systems could provide South Africa with the requisite knowledge on viral prevalence and infectivity to manage the risk effectively.

“The programme [provides] us [with] a toolbox to monitor exactly how we engage our interventions around this pandemic, monitor the course of the pandemic and engage the issue of the efficacy of our interventions over this time,” he says.

Given the varied water and sanitation services delivery mechanisms in South Africa, there is a need for an all-encompassing water- and sanitation-focused approach to the surveillance of the Covid-19 spread in less developed countries.

The prevalence of intermittent water supply and environments with limited or no drainage infrastructure, as well as inadequate and improper nonsewered sanitation systems, increases the exposure of many communities to the virus.

The South African approach will look at both wastewater and off-grid faecal sludge samples to cover both urban communities with centralised wastewater services and marginalised communities in informal, rural and water-constrained settlements that use a combination of on-site and nonsewered sanitation systems.

Liphadzi points out that the programme can enable South Africa to measure the scope of the outbreak and determine the hot spots and whether the wastewater systems – sewered and nonsewered – are potential infection points, owing to occupational exposure.

“There is a lot we do not know about the Covid-19 virus, and several research initiatives are being undertaken internationally to answer the same concern we all have regarding how long the virus can survive in the wastewater and sanitation environment and the conditions under which this occurs.

“If the virus does survive in wastewater and sanitation samples, understanding the level of risk posed to communities and implementing key strategies that involve an early-warning alert of potential communal spread will be critical.”

It will also provide decision-making support and determine the timing and severity of public health interventions to mitigate the spread of the virus and better anticipate the likely impact and inform hospital readiness and the necessity of public health interventions.

The WRC intervention comprises three phases, the first being the establishment of the proof of concept of the presence of Covid-19 in wastewater and sanitation samples, as well as establishing sample collection and testing protocols so that monitoring results can be reliable and compared.

WRC drinking-water quality and treatment research manager Dr Nonhlanhla Kalebaila says the project will kick off with the proof of concept phase over the next month to four months, followed by pilot-scale monitoring and then nationwide surveillance.

The proof of concept will cover sample design, testing sampling protocol and preliminary characterisation, as well as the risk of infection in wastewater treatment plants.

The second phase will include the pilot-scale monitoring of provincial hot spots and the preliminary pilot surveillance monitoring data, in addition to establishing wider capacity of laboratories in South Africa and incorporating more communities into surveillance over a period of six months.

The third phase over the next year to three years will comprise national wastewater surveillance and includes full-scale national sewershed surveillance, data analysis, integration, communication and research with sector and government support.

The programme can also form part of a larger initiative integrating water quality and sanitation health, as well as security of supply, Naidoo says.

Improving the techniques of wastewater monitoring as a mechanism for the long-term surveillance of Covid-19 in South Africa’s popu- lation and communities will have far-reaching impacts on the nation’s capacity and resources in dealing with the disease.

“The idea of creating a countrywide GIS-based heat map to first act as a triage mechanism to better direct the resources of the Department of Health for on-the-ground testing as a low-cost community-level indicator is very attractive,” the WRC concludes.