Wastewater and the spread of COVID-19

For ten years, Caroline, a kale ‘sukuma wiki’ vendor in one of Nairobi’s busiest markets has been receiving healthy-looking kale from her supplier. However Caroline does not know where her vegetables are grown or whether the farmer uses clean or untreated sewer water for the crops. For many years, Kenyans living in urban areas, and especially in Nairobi, have been warned that fruits and vegetables sold in markets could have been grown using wastewater.

New scientific evidence detected the presence of SARS-Cov-2 RNA, the virus that causes COVID-19, in wastewater systems, indicating a possible fecal-oral transmission route. In response to this finding, researchers from developed countries have employed wastewater-based epidemiology [1] as a methodology for detecting the prevalence of the virus in the population within a sewer catchment. Though studies have not confirmed any known cases transmitted from wastewater to humans, the potential for aerosolized transmission of the virus disseminated by wastewater sprinkler irrigation systems is a possibility.

The Nairobi’s Shit Flow Diagram (SD)[2], developed with support from African Population Health and Research Centre (APHYRIC), estimates that only 34 percent of excreta in Nairobi is treated. The remaining two-thirds is disposed of raw or left in the open environment, flowing through rivers, where it is tapped and used to irrigate more than 760 hectares of land.

Wastewater irrigation in Nairobi

The National Environmental and Management Agency (NEMA), Kenya’s watchdog on environmental protection, requires that wastewater is treated to acceptable levels before disposal or re-use. However, cases of wastewater irrigation in Nairobi and its environs have been documented in recent years. There are three main instances of wastewater being used for irrigation. The first is the informal settlements where residents ‘eat their own shit’ – a metaphor used to describe the consumption of vegetables grown from the direct use of untreated wastewater.

The second category of wastewater use is farmers who cultivate vegetables in areas downstream of the Nairobi River, such as the towns of Athi-river and Mlolongo located in the southeast area of Nairobi, where the soil and water are contaminated with waste from industrial effluents and municipal sewers. Knowingly or unknowingly, the farmers use wastewater to irrigate their farms. Most of these vegetables end up in local retail stores within Nairobi City.

The final instance of wastewater irrigation in Nairobi is the use of partially treated wastewater flowing from a semi-functional sewer treatment plant in a high-income residential area. High-income neighborhoods in Nairobi attract illegal settlers in private or unused public land who provide cheap labor to residents. The settlers cultivate crops using the wastewater discharged from affluent homes. Farmers growing in encroached lands or vendors selling crops grown in these areas irrigate and wash their produce in water channels filled with wastewater. In such situations, a symbiotic relationship develops, where the informal settlers get "free" water with high nutrient content for their farms, while wealthy residents discharge waste cheaply, with little to no investment channeled to the construction of functional wastewater treatment plants.

These farmers are constantly exposed to wastewater and consume produce directly from their farms. Consumers who buy from encroached farms, most of whom are from low- to medium-income families, are also exposed to the virus and other enteric diseases that can be potentially transmitted by the handling of contaminated vegetables. In stark contrast, the wealthier residents surrounding these farms benefit from well-maintained plumbing works that delineate their dwellings with the contagion loads present in nearby wastewater irrigation farms.

The inequitable spread of COVID-19 in Nairobi

The groups with the highest exposure to SARS-CoV-2 are mostly landless farmers and their families from low socioeconomic groups. According to the World Health Organization (WHO)[3],  cases in lower social-economic groups are more likely to be severely ill and die from COVID-19, as their immune systems are already weakened by other enteric diseases associated with wastewater.

Despite a lack of quality data in assessing health outcomes between social and/or economic groups, disparities in COVID-19 infections may, now and in the future, be used to describe entrenched inequalities. It is also increasingly clear that wastewater use is entrenching health inequalities. Mortality and infection rates from COVID-19 disease reported in poorer populations could now and in the future be mediated by wastewater management practices in higher-income groups.

USAID's interventions in WASH

To reduce the health inequalities associated with access to proper sewerage systems in Nairobi, USAID’s Kenya Integrated Water, Sanitation and Hygiene (KIWASH) project is working with small, private WASH enterprises, especially those operating in informal settlements, to close the service gap and improve sanitation services levels in areas beyond the reach of the city’s sewerage network. This includes providing business development support and small infrastructure improvements to expand sanitation in underserved areas. The Gatwekera Tosha sanitation enterprise, for example, which operates in Kibera, Nairobi’s largest informal settlement, is one of the many successful groups that have recently expanded access to sanitation services for 809 households.

In collaboration with the Nairobi County government, the KIWASH project helped form the Sewer and Sanitation Revolving Fund Policy (SSRF), a legal instrument that aims to enable the county government to mobilize resources from numerous private-public partnership arrangements, development partners, equalization funds, NGOs and more to achieve 100% improved sanitation service coverage by 2030. The overall target in the short- and medium-term is to raise US$1 billion in funding for sanitation infrastructure development.


The current wastewater management situation in Kenya makes it impossible to detect the prevalence of SARS-CoV-2 infection at a given geospatial location. As public health professionals work to contain the pandemic, the government must reduce wastewater irrigation methods that lead to widespread airborne droplets or aerosols landing on surfaces and public spaces. The immediate strategies should include:

  • Improving risk communication on the potential of wastewater to increase COVID-19 infection, especially among those groups most at risk.
  • Developing sound policies that offer environmental and health protection for all. In particular, the government should pass and enforce a measure that ensures food hygiene and the use of protective gear for wastewater workers and farmers.
  • There are also immediate opportunities to regulate, finance, enforce and work with private entities, development partners, and communities to improve the operations, maintenance, and efficiency of non-networked sewers.
  • Finally, it is also time to acknowledge the potential role of higher social-economic groups in sustaining and propagating health inequalities and COVID–19 infections. We should curtail insidious explanations in media and scientific research, dominantly featuring wastewater use for irrigation by low-income groups without addressing the structural problems rooted in higher social-economic groups.

Together, these strategies could help reduce COVID-19 and other illnesses, especially among those most potentially exposed to the virus through untreated wastewater.


  1. Ahmed W, Angel N, Edson J, Bibby K, Bivins A, O'Brien JW, et al. "First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community." Science of The Total Environment. 2020:138764.
  2. La Rosa G, Iaconelli M, Mancini P, Ferraro GB, Veneri C, Bonadonna L, et al. "First detection of SARS-CoV-2 in untreated wastewaters in Italy." Science of The Total Environment. 2020:139652.
  3. Xiao F, Tang M, Zheng X, Liu Y, Li X, Shan H. "Evidence for gastrointestinal infection of SARS-CoV-2." Gastroenterology. 2020;158(6):1831-3. e3.
  4. Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, et al. "SARS-CoV-2 viral load in upper respiratory specimens of infected patients." New England Journal of Medicine. 2020;382(12):1177-9.
  5. Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, et al. "Detection of SARS-CoV-2 in different types of clinical specimens." Jama. 2020;323(18):1843-4.
  6. Wu Y, Guo C, Tang L, Hong Z, Zhou J, Dong X, et al. "Prolonged presence of SARS-CoV-2 viral RNA in faecal samples." The Lancet Gastroenterology & Hepatology. 2020;5(5):434-5.
  7. K PE, C OKB, Chao-Sheng T, Ken C, J R-C, Hossam A-N, et al. "Post COVID-19 Water and Wastewater Management to Protect Public Health and Geoenvironment." Environmental Geotechnics. 0(0):1-14. doi: 10.1680/jenge.20.00067.


[1] Wastewater-based epidemiology is the analysis of wastewater to identify the presence of biologicals or chemicals for the purpose of monitoring public health. More information is available at https://iwa-network.org/learn/covid-19-wastewater-based-epidemiology/.

[2] A Shit Flow Diagram (SFD) is a model developed to visualize excreta management in cities. Additional information is available at  http://www.sanergy.com/2018/12/04/the-sfd-a-new-way-of-visualizing-excreta-management-in-nairobi-city/.

[3] WHO Webinar – “Inequities in COVID-19 infection and mortality: socioeconomic risk factors and populations at risk.” The information available at https://www.who.int/news-room/events/detail/2020/11/04/default-calendar/who-webinar---inequities-in-covid-19-infection-and-mortality-socioeconomic-risk-factors-and-populations-at-risk

About the author

Diana Mulatya is currently (2021) KIWASH Sanitation and Hygiene Advisor. She has over ten years of experience in connecting research with practice and providing advisory services in Kenya’s Water, Sanitation, and Hygiene sector. She holds a master’s degree in Public Health, from the London School of Hygiene and Tropical Medicine. She has worked with local and national governments, private sector players, not-for-profit organizations, United Nations agencies, and bilateral and multilateral donors such as USAID, UNICEF, DFID. She holds a key interest in the health and market development of sanitation and hygiene services and has co-authored different peer-reviewed publications for marginalized communities.

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