OPINION | Monitoring Covid-19 using poop: What about non-sewered settlements?

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The wastewater treatment plant at Camps Bay pumps over two million litres of raw sewage out to sea every day.
The wastewater treatment plant at Camps Bay pumps over two million litres of raw sewage out to sea every day.
Steve Kretzmann/WCN

Around the world scientists have been tracking genetic material of the coronavirus in sewer systems. Sudhir Pillay, Chantal Ramcharan-Kotze and Jay Bhagwan write that this is an issue when it comes to non-sewered sanitation systems, which are found in South Africa.


The year 2020 has been dominated by the news of 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 that either come from infected patients or surfaces. Social distancing measures, regular handwashing and the use of masks have been implemented as measures to reduce disease transmission. Despite these measures, 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 the tracking of the disease. Lockdown measures – to limit unnecessary human-to-human contact – have been introduced globally during infection peaks.

In Europe, many countries are experiencing a second wave and governments are implementing lockdown measures to mitigate disease transmission. 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 sewer systems.

Using the knowledge that infected patients shed the virus in stools and urine, scientists could detect the genetic material of the virus at wastewater plants. The detection of the genetic material of the virus did not indicate whether the virus was viable i.e. infectious.

Patient admission curve line

Using this information, scientists led by Yale University in the US, 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 to understand when peaks occur. In Italy, wastewater scientists, using wastewater samples that were 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 to determine 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, developing a wastewater surveillance programme that has the potential to be linked to disease outbreak tracking.

Jay Bhagwan, executive manager of Water and Wastewater Futures at the WRC, said: "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 sewer systems offer the opportunity to possibly track Covid-19 outbreaks within the boundary of a specific sewer network, many developing countries including South Africa, are characterised by a mixture of sewered and non-sewered sanitation systems.

READ | Analysis: Monitoring our wastewater: Covid-19 is in our poop

Globally, around two billion people rely on non-sewered sanitation systems, mostly in developing countries.

Non-sewered systems include septic tanks, various latrine systems – known as long-drop 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 metro 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 that have a mixed approach to sanitation technologies, the WRC and the 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 previously discussed 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 means of developing a Covid-19 surveillance tool.

"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 Water Research Commission is aimed at contributing to public health and understanding disease outbreaks," explains Kim Nøhr Skibsted, executive director at Grundfos Foundation.

There are a number of benefits of developing a water quality-based surveillance tool for non-sewered settlements.

Early warning system

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 grey water – washing water - and faecal waste, and generally represent the more vulnerable members of the population which 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 the 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.

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


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