Tracking Covid-19 in the sewer system of South Africa’s informal settlements could expand our knowledge base

By Sudhir Pillay, Chantal Ramcharan-Kotze and Jay Bhagwan 17 November 2020

Newly built homes in Ethembeni informal settlement covered in sewage water after a sewage pipe burst. (Photo: Gallo Images/Brenton Geach)

The monitoring of water samples from formal sewerage systems for Covid-19 has rapidly become standard practice globally. Now a South African project is expanding that to monitor sewage discharge in non-sewered areas – informal settlements.

The year 2020 has been dominated by the Covid-19 pandemic. The disease is caused by a new coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The scientific community has indicated that the main mechanism of disease transmission is through contact with respiratory droplets from infected patients and surfaces that have viable virus particles. Social distancing measures coupled with regular handwashing and the use of masks have been implemented as measures to reduce disease transmission. Despite this, waves of outbreaks have been observed globally.

In South Africa, the first wave of the outbreak has nearly concluded in most provinces based on data obtained from individual testing and tracking of the disease. Lockdown measures – to limit unnecessary human to human contact – have been introduced globally when there are peaks in infection. In Europe, many countries are experiencing a second wave of Covid-19 transmission with governments implementing lockdown measures as a means of disease transmission mitigation. But are there other means of forecasting these peaks in Covid-19 transmission, in addition to individual testing, to enable improved mitigation strategies?

Wastewater scientists around the world have been tracking the genetic material of the virus in the sewer systems. Using the knowledge that infected patients shed the virus in their stools and urine, scientists can detect the genetic material of the virus at wastewater plants. The detection of the genetic material of the virus does not indicate whether the virus is viable, i.e. infectious.

Using this information, scientists led by Yale University in the US have positively correlated the Covid-19 patient admission curve with the quantity of genetic material of SARS-CoV-2 detected at a wastewater plant at a specific geolocation. Many countries have begun a Covid-19 wastewater surveillance programme as a means of tracking disease progression and understanding when peaks occur.

In Italy, wastewater scientists using wastewater samples that had been previously collected detected the virus genetic material before the first outbreak occurred in that country. The results highlight the usefulness of tracking the virus in wastewater and complementing individual testing as a means of understanding outbreak patterns.

In South Africa, the Water Research Commission (WRC) has recently concluded a proof-of-concept study in determining whether the genetic material of the virus is present in the sewer system in selected cities. Following the detection of the genetic material of the virus at appreciable levels, the WRC and partners will further this research into developing a wastewater surveillance programme that has the potential to be linked to disease outbreak tracking. Our proof-of-concept study has shown the presence of the genetic material of the virus that causes Covid‑19 at selected sites. Using this knowledge and observing the developments occurring across the world, there exists the potential to use wastewater as a Covid-19 surveillance method that could complement existing disease tracking platforms.

While sewered systems offer the opportunity to possibly track outbreaks within the boundary of a specific sewered network, many developing countries including South Africa are characterised by a mixture of sewered and non-sewered sanitation systems. Globally, around two billion people rely on non-sewered sanitation systems, mostly in developing countries.

Non-sewered systems include the septic tanks, various latrine systems – known as long-drops to the general public – and other forms of sanitation that are not connected to a sewer system. In South Africa, around four million households use latrines for their sanitation needs and there is no single metropolitan in South Africa that is 100% sewered. This represents a significant number of the population that cannot be covered by the current Covid-19 wastewater surveillance tool.

To address this gap and understanding that developing countries have cities with a mixed approach to sanitation technologies, the WRC and the philanthropic Grundfos Foundation have partnered to develop a water quality-based surveillance tool for non-sewered settlements as part of a city-wide approach that will complement the wastewater surveillance programme and in turn provide support to other means of tracking disease outbreaks.

Appreciable levels of genetic material of the virus that causes Covid-19 have been detected in samples recovered from a single non-sewered settlement that was undertaken during the proof-of-concept study. The next phase of research undertaken with financial support by the Grundfos Foundation aims to determine if the virus genetic material can be detected in other non-sewered locations across South Africa and develop a surveillance approach which could be used by other developing countries.

To our knowledge, it is the first large-scale programme being undertaken globally that will monitor SARS‑CoV-2 in water and sanitation samples collected from non-sewered settlements as a means of developing a Covid-19 surveillance tool. As Kim Nøhr Skibsted, executive director of the Grundfos Foundation explains, “with Covid-19 threatening global health, it is more important than ever to prevent disease from spreading among society’s most vulnerable. The partnership between the Grundfos Foundation and the WRC is aimed at contributing to public health and understanding disease outbreaks.”

There are a number of benefits for developing a water quality-based surveillance tool for non-sewered settlements. First, most developing countries and their cities are served by non-sewered sanitation technologies. These areas generally do not have sewer systems to dispose of greywater – washing water – and faecal waste and generally represent the more vulnerable population who have limited financial resources and live in densely-packed non-regulated areas, where the use of shared ablution facilities is common.

Second, if the virus genetic material is detected in significant quantities, the data could be used to provide an early warning system in densely populated non-sewered areas in which social distancing is challenging and therefore the disease transmission risk is potentially high. The development of a non-sewered sanitation Covid-19 surveillance tool can complement sewered wastewater surveillance as part of a city-wide water quality-based surveillance approach and develop a knowledge base that can provide a better understanding of Covid-19 spread within countries. DM

Sudhir Pillay, Chantal Ramcharan-Kotze and Jay Bhagwan work for the Water Research Commission.


Comments - share your knowledge and experience

Please note you must be a Maverick Insider to comment. Sign up here or if you are already an Insider.

Everybody has an opinion but not everyone has the knowledge and the experience to contribute meaningfully to a discussion. That’s what we want from our members. Help us learn with your expertise and insights on articles that we publish. We encourage different, respectful viewpoints to further our understanding of the world. View our comments policy here.

No Comments, yet


Days of Zondo: ANC and Joburg mayor Geoff Makhubo plunged into EOH tender kickback scandal

By Tebogo Tshwane