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Photo essay: Sewersheds: What can wastewater tell us about community health?


One of the major challenges during the COVID-19 pandemic was the difficulty of interpreting the testing data. Conventional laboratory testing of persons with symptoms may be limited because it is expensive, some people are more likely to get themselves tested than others, many people do not get tested because they are asymptomatic, and data from those who do get tested only becomes available some time after the test. In response to these limitations an unconventional idea has emerged: would it be possible to get a sense of infection levels by monitoring wastewater? This would have the advantage of providing information for whole populations in near real-time. The Gauteng City-Region Observatory has been working with the National Institute for Communicable Diseases to understand the link between wastewater surveillance, conventional laboratory testing of symptomatic persons, population dynamics and impacts on society.

This photo essay tells the story of how wastewater is treated in two parts. Part 1 of the photo essay looks at our sewer systems and how wastewater is treated. Part 2 shows how this wastewater is analysed to measure the burden of COVID-19 or other diseases. This full process is shown in the process diagram in Figure 1.


Figure 1: Wastewater treatment for a sewershed in Gauteng and the role wastewater surveillance plays in public health intervention.

The high density of people that comes with urban living has necessitated the creation of sophisticated sewerage systems. Without systems to remove and treat wastewater, human and environmental health twould be substantially compromised. Wastewater that flows through the sewer system can be transported either through gravity flow (flow from a high elevation to a lower point) or pumped through the pipes with pump stations where gravity flow is not possible.

Most people are familiar with the term 'watershed' (Parker et al., 2017) meaning 'an area or ridge of land that separates waters flowing to different rivers, basins or seas' (South African Concise Oxford Dictionary 2002). The term sewershed is less familiar, but borrows the idea of the watershed to help us imagine sewerage networks. Across Gauteng there are a series of separate networks - shaped in part by the geography of the city region - through which wastewater is collected. A sewershed is the area of land where all the sewers flow to a single wastewater treatment work. They can be large or small, depending on the community they serve and the capacity of the wastewater treatment works. But we're also interested in sewersheds because they can be used to give us measures of the presence of various kinds of diseases in the populations they serve.

Part 1: What is a sewershed and how is wastewater managed?

The sewer network is a hidden infrastructure, with most of the pipes buried underground. No one wants to think about what happens with the water and waste after they've flushed it. The water and waste that flows within the sewer pipes is called sewage. Sewage includes wastewater, trade effluent from industry or manufacturing where allowed, standard domestic effluent and other liquid waste, either separately or in combination. Stormwater overflow is not intended to flow into sewersheds, but rather into natural topographical drainage points such as rivers and lakes, or constructed stormwater drains or outflows. The sewer network is a collection of pipes and sewers that work together to collect and drain wastewater from the population to a wastewater treatment facility. Typically, small pipes leave our homes and buildings, and connect to a bigger pipe to transport the sewage to the treatment plant. Maintenance holes (manholes) are used for routine inspection and repairs when these pipes are blocked or broken or to monitor the state of the sewer network.

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Photo 1: A sewer maintenance hole provides access to the underground sewer pipes. All these pipes flow to the wastewater treatment plant.


Photo 2: Wastewater from communities flowing in the maintenance holes.

How is human waste connected in a sewershed?

Gauteng has a complex infrastructure for wastewater across the city-region. Toilets are used to connect waste across our homes, businesses and industry. The only toilets connected to the sewer system are water-borne flush toilets. These toilets are typical in cities where there is a high density of people. Toilets are flushed with potable water (water that is clean and drinkable), and sewage (urine and faeces) enters the sewage line through underground pipes.




Photo 3: Examples of toilets throughout Gauteng.

In Gauteng province, both affluent, middle and lower income settings are connected to the sewage system. Flush toilets are connected to a piped network. When you flush your toilet, the water and waste flows into an underground pipe from your house into a bigger pipe, where waste from all the houses are mixed and flows to the wastewater treatment plant. If you look carefully in streets or on pavements in these urban areas, you can see the maintenance hole covers of the sewage system which are usually, located in lines approximately 250-500m apart.


Photo 4: Communities and houses that are connected to the sewer system in the Gauteng City-Region.


Photo 5: A broken sewer pipe with sewage leaking in the environment. Infrastructure maintenance remains a challenge in many parts of Gauteng.

Some main sewer pipes in Gauteng are more than 3m in diameter - big enough for a small vehicle to drive through.

How is wastewater treated?

Wastewater flows from communities via sewer pipes to a wastewater treatment plant where it is processed and treated before being released back into the environment.

Wastewater treatment cleans the water to an acceptable standard so that it can be safely released back into the environment, usually into a stream or river. The contaminants in wastewater are removed by physical, chemical, and biological processes through primary and secondary treatment (Hansen, 2015). Not all wastewater treatment plants work in the same way. Here we discuss a treatment process at one of the City of Tshwane’s Wastewater Treatment Works, close to the City Centre. Primary treatment includes screening and primary settling. The wastewater treatment process can differ in different plants or municipalities depending on the composition of the wastewater and available technologies.

Primary wastewater treatment

On entry to the treatment works, wastewater flows into a canal for treatment.


In the first step all the visible solids are removed from the wastewater by screens and grit removal systems. This includes any pieces of wood, rags, cans, sand, egg shells, sanitary products (such as tampons, pads, and diapers) and condoms.


Photo 6: Screens used to remove visible solids, such as rags and cans.


After visible impurities are removed through screening and grit removal, water is pumped into a primary settling tank. From the surface, these are circular or cylindrical tanks that are open at the top. Actually, they have hidden cone-shaped bottoms that allow the solids to settle at the bottom and liquids overflow at the top. Between 40% and 60% of suspended solids (small particles that remain suspended in the water) are removed in this step. Solids that settle at the bottom of the tank are sent to a digesting tank while the liquids are sent to the secondary treatment process.


Photo 7: Primary settling tank where solids sink to the bottom and liquid overflow are pumped towards the secondary treatment process.

Secondary wastewater treatment

Many dangerous pathogens (microorganisms that can cause disease) live in wastewater, for example Vibrio cholerae or Salmonella Typhi. These must be removed before water is released into the environment. There are also many excess nutrients in the water which could damage the environment, including phosphorus and nitrogen/ammonia. Most of these come from the organic material in our waste including undigested nutrients and food waste, and from cleaning materials found in wastewater from washing machines and kitchen sinks. These nutrients cause an unnatural increase in plant and algae growth (known as eutrophication). If left untreated these cause severe damage to our aquatic environments. There are many processes available to remove these, but we only describe the activated sludge process, as it is the most common process in municipal wastewater treatment.

Activated sludge

This process is used to remove excess nutrients in the water. Water from the first primary treatment is mixed with activated sludge, (a pool of microorganisms used to remove excess nutrients) in an aeration tank. The contents of the tank are mixed vigorously to aerate the mixture. These microorganisms digest and consume the excess nutrients in the wastewater, and restore the nutrient concentrations to acceptable levels.

The mixture is then pumped to a secondary settling tank to allow for solids to settle once more. Some of these solids are pumped back to the aeration tank to ensure the microorganism pool is kept constant, while the rest is discarded as waste. The water overflow in the settling tank is assumed to be almost free of suspended solids and is pumped to the disinfection station.


Photo 8: Activated sludge tank being aerated for nutrient removal.

Disinfection and release back into the environment

In the final step of wastewater treatment, water is disinfected with chlorine gas to eliminate pathogens present in the water. The overflow water from the secondary treatment step flows into a canal, where it is mixed with chlorine gas. The chlorine gas removes all harmful pathogens from the water.

The water that has been disinfected with chlorine is tested in a laboratory before it is released into the environment (a river or dam) to ensure that the treatment process removes all the nutrients (nitrates and phosphates) and harmful pathogens. After disinfection and testing the water quality, the water is released into a natural water source or a receiving water body. In some cases water is also pumped to zoos, golf courses or used for irrigation.


Photo 9: Treated water, disinfected with chlorine gas, flowing to the Apies River.


Photo 10: Laboratory personnel testing the treated water.

There is a specific standard to which water must comply before released into the environment. This is called the Green Drop status. No wastewater treatment plant in South Africa qualified for the Green Drop status certificate in 2021 which is the most recent report issued by the Department of Public Works (Department of Public Works, 2022).

What happens to the solids from the wastewater?

All solids from the primary settling steps are pumped into tanks and treated further. There is no oxygen in these tanks, and microorganisms remove nutrients by anaerobic digestion. Anaerobic digestion will help microorganisms digest nutrients without oxygen, and produce methane. Methane is an odourless, colourless and flammable gas which is extremely poisonous to humans. This gas can be used to generate electricity and many wastewater treatment plants in South Africa are exploring the possibilities of alternative energy generation. If the solids are not digested in this way, they will not be stabilised and will produce bad odours and attract flies. After digestion, solids are placed in dry beds and are dried by the sun to produce compost. This compost is free for the public to use after permission has been granted.


Photo 11: Anaerobic digestion tank.


Photo 12: Dried solids to be used as compost.

Part 2: How can wastewater be used to measure infectious diseases within a community?

The COVID-19 pandemic has prompted scientists and policy makers to use environmental surveillance as a means to respond to public disease outbreaks. Environmental surveillance can be used to monitor infectious diseases (National Institute for Communicable Diseases, 2023) which are diseases which can be transferred from one person to another, and cause illness, such as influenza, COVID-19 or hepatitis A. The measurement of pathogen levels in wastewater is one example of environmental surveillance that has gained in popularity as a potentially affordable way to monitor whole populations near real-time. Wastewater monitoring has the benefit that one does not need to collect clinical data from individuals, which is often time consuming and expensive. How would this work in practice?

Collecting wastewater for analysis

The pipe that carries wastewater from the community flows to the wastewater treatment plant, where it is treated. Before the wastewater is treated, a small sample (1L) is collected weekly from a maintenance hole or the wastewater treatment plant. The sample is transported to the laboratory on ice to ensure that the virus particles do not degrade before it is tested, resulting in a false negative result (a negative test result that is actually a positive result).


Photo 13: Lethabo Monametsi, an employee of the NICD Wastewater Genomics Syndicate collecting a sample from a maintenance hole in the Gauteng City-Region.


Photo 14: Mokgaetji Macheke, a laboratory scientist who works for the NICD Wastewater Genomics Syndicate, processing the sample brought by Lethabo. Mokgaetji will test this sample for virus particles in the wastewater.

Laboratory testing of influent wastewater for diseases of interest

In the laboratory, the virus particles in the sample are concentrated for easier detection. A polymerase chain reaction (PCR) test is done to determine the presence of the virus in the sample. If the virus is present, the DNA (or RNA) can be sequenced to determine the variant or lineage of the virus that is present in the sample.

The samples are processed like this. First, the genetic material that is present in the sample (RNA or DNA) is extracted from the concentrate. This is done by breaking down or dissolving the biological material in the sample, and adding a substance such as customised magnetic beads or a fibre that traps or binds RNA or DNA. Everything that is not bound is washed away, leaving only the genetic material. Then a PCR test is done.


Photo 15: Mokgaetji Macheke, testing the sample with a PCR test.

This includes heating the sample to separate (or ‘unzip’) the two complementary chains or double-stranded structure of DNA that is present in the sample. Then, special starter molecules called primers are added to the mixture. These primers are chosen to have a DNA sequence that is specific to the pathogens we are interested in. While the sample may contain DNA or RNA from many different microorganisms, the primers will only attach to DNA/RNA that has the sequence of the pathogen we choose. To detect the SARS-CoV-2 virus (the virus responsible for COVID-19 disease), we use primers that look for the N-gene, a part of the virus that is abundantly present and well preserved in wastewater. Next, using the primers as starting points, an enzyme called DNA polymerase copies the original DNA strand from the sample to make new strands of DNA. We call these new strands ‘amplicons’. This process is repeated many times, doubling the copied DNA each round. This amplification is exponential and allows very small amounts of original RNA or DNA to be made into very many copies. The last step in a PCR test is to detect and quantify the amplified products to be sure that they are from the pathogen we are looking for. In a real-time PCR reaction, we use probes with fluorescent dyes. The probes have specific DNA sequences that are found in the SARS-CoV-2 N-gene. When they bind to the amplified targets, they fluoresce and are detected by a light-sensitive metre in the PCR machine.


Photo 16: Mokgaetji Macheke testing the sample for diseases.

From these results, we can determine the exact concentration of SARS-CoV-2 in the original sample and understand which SARS-CoV-2 variants are present in the wastewater. The results are expressed in ‘genome copies per millilitre of wastewater’ and are specific to the sewershed from where the sample was taken. From the concentration of virus in the wastewater sample, we can determine the amount of virus circulating in the population, and the true burden of disease present in the communities feeding into the sewer pipe. The next steps of this project will look at these results in different communities and social circumstances within Gauteng.


Photo 17: A centrifuge used in the testing process.

Measuring the impact of the COVID-19 pandemic from wastewater data


Photo 18: Aerial photo of the City of Tshwane’s Wastewater Treatment Plant, close to the City Centre. Credit Clive Hassell.

The next steps of this project are to understand the relationship between the laboratory results from wastewater monitoring in different communities in Gauteng. The Gauteng City-Region Observatory is currently collaborating with the National Institute for Communicable Diseases, the South African Centre for Epidemiological Modelling and Analysis and the London School of Hygiene and Tropical Medicine on the use of wastewater data to measure for infectious diseases. Wastewater can be used as a method to monitor trends in diseases, early warning systems, and study genetic diversity in pathogens. The aim of this project is to correlate socio-economic data, spatial form of the city to burden of disease to better inform public policy.


This project is a joint NICD and GCRO collaboration. We would like to acknowledge and thank the Water Research Commision (C2020-2021-00669) as well as the Bill and Melinda Gates Foundation (INV036531, INV049271, INV050051) for funding this project. We would also like to acknowledge the National Institute for Communicable Diseases, Kerrigan McCarthy and Sibonginkosi Maposa for the technical inputs, project leadership laboratory access and for accompanying the team on site visits. Thank you to Mokgaetji Macheke, and Lethabo Monametsi for helping with the photos.

Thank you to the City of Tshwane’s Wastewater Treatment Works, close to the City Centre, and Funani O.Ramalamula, Destiny Ditshwanelo Phalama and Willie Els for educating us on the works of the wastewater treatment plant.


Department of Water & Sanitation and Department of Public Works (2022) Green Drop Report 2022.

Hansen, K. (2015) Overview of Wastewater Treatment in South Africa. Limpopo, South Africa: Association for Water and Rural Development.

National Institute for Communicable Diseases. 2023. Wastewater-Based Epidemiology For Sars-Cov-2 In South Africa Including Wastewater Genomics.

Parker A, Maree G, Khanyile S, Culwick Fatti C. 30 August 2017. Watershed boundaries of the GCR. . Date accessed 22 August 2023.

All photographic credit goes to Tshepiso Seleka (@thedarkroomartist).

Edits and input: Kerrigan McCarthy, Richard Ballard and Graeme Gotz

Infographic design: Leith Davis

Suggested citation: Els, F., Seleka, T. and Maree, G. (2023). ‘Sewersheds: What can wastewater tell us about community health? Photo Essay: Gauteng City-Region Observatory. September 2023.


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