Global Waters
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Global Waters

Using Wastewater Surveillance to Monitor COVID-19

November 2020- Hana Muhaisen, a lab Technician at Water Authority of Jordan Labs, is processing a sample into the Refrigerated Centrifuge equipment which was supplied by USAID. Photo credit: USAID Jordan Water Infrastructure Activity

As we enter the third year of the COVID-19 pandemic, many national and local governments are turning to a surprising source of data to track the latest surge of the virus: pathogens in the wastewater in their sewage systems.

This approach has long been used to help monitor the spread of diseases such as polio and typhoid, notes Joe Brown, an associate professor of environmental sciences and engineering at the University of North Carolina at Chapel Hill and principal investigator of the Maputo Sanitation (MapSan) trial.

“For about 100 years, we’ve been looking for pathogens in wastewater as a way of informing public health response,” he says. “And the data can complement clinical data in a variety of ways — for example, to generate data on infections that are primarily asymptomatic and therefore may be underestimated in other health surveillance.”

COVID-19 often goes undetected because it leads to mild or no symptoms in many people, and thus can spread quickly. The rise of the highly contagious Omicron variant has swamped testing resources in countries throughout the world, widening the gap between reported and actual cases.

Monitoring of COVID-19 in wastewater can inform health authorities by providing community-level data on trends in infections. The SARS-COV-2 virus that causes COVID-19 is shed in people’s feces, offering a source of data that does not depend on access to testing, healthcare-seeking behavior, or timely reporting of results.

Wastewater surveillance can identify COVID-19 hotspots, provide early warning of new outbreaks, and confirm trends in clinical data. Given these considerations, USAID launched a new activity under the Jordan Water Infrastructure project to enhance the Jordanian government’s capacity to conduct wastewater surveillance for COVID-19.

Wastewater surveillance systems offer the possibility of earlier detection and rapid response to spikes in COVID-19 and new variants. In many cities, the surveillance data are being used to monitor the trajectory of the Omicron surge and determine when it has peaked. And some governments and universities have used these data to target testing services, refine health messages, and forecast clinical resource needs.

A global map maintained by the University of California Merced showed that by the end of March 2022, wastewater was being monitored for the virus in at least 3,393 sites in 64 countries. Almost two-thirds of those sites are in high-income countries, but wastewater surveillance can be even more useful in settings with limited resources for clinical surveillance, notes Brown, who is working with Mozambique’s national sequencing laboratory to add wastewater monitoring to its surveillance of COVID-19 variants in the city of Maputo.

Most households in Mozambique and other low- and middle-income countries are not served by sewer systems, but this lack of infrastructure may not be an insurmountable obstacle to community-level monitoring of COVID-19 and other pathogens, Brown adds. “What we need to do now is to adapt tools that can be applied at scale,” he says. “That means using these same methods on fecal sludges, impacted surface waters, drains, and other environmental matrices that are not wastewater but still contain fecal contamination.” A pre-COVID study among clusters of households participating in the MapSan trial suggests this approach holds promise for pathogen surveillance.

November 2020— Hana Muhaisen, lab Technician at Water Authority of Jordan Labs, and Rawan Abu Eita, CDM Smith representative, processing samples taken from a sewer manhole to test for genetic material in wastewater. Photo credit: USAID Jordan Water Infrastructure Activity

In Jordan, where more than 60 percent of the population is connected to a sewer system, Water Authority technicians began testing for SARS-COV-2 genetic material in wastewater in June 2020. However, they did not have a monitoring plan and lacked the necessary capacity for speedy processing of large numbers of tests.

USAID’s Jordan Water Infrastructure project worked with the Water Authority and the Ministry of Water and Irrigation to develop that capacity. Conducted from August 2020 to March 2021, this pilot project resulted in a doubling of the Water Authority of Jordan’s capacity to process wastewater samples for COVID-19 measurement.

The pilot began with the development of a plan for COVID-19 surveillance in the Ain Ghazal sewer system, which serves more than 2 million people in the city of Amman. The plan identifies locations for obtaining wastewater samples, outlines different levels of monitoring to be conducted based on clinical data, and includes actions to be taken when COVID-19 is detected at one of the monitoring locations.

USAID purchased the equipment and supplies required to improve testing sensitivity and efficiency at the Water Authority’s virology laboratory. Through practical training, the project developed the skills of the Water Authority technicians in all aspects of wastewater surveillance, from sample collection to analysis and reporting.

Water authority staff involved in the activity also received training in COVID-19 health and safety protocols to ensure safe handling of wastewater samples. (Although the virus shed in wastewater has not been shown to be infective, the use of personal protective gear and other precautions are recommended).

November 2020 — Islam Asi, sample handler from Water Authority of Jordan Labs, and Bashar Khalil, CDM Smith representative, collecting samples from a sewer manhole outside the Ain Ghazal Pump Station Photo credit: USAID Jordan Water Infrastructure Activity

The lessons from the Ain Ghazal pilot project were shared during a virtual workshop on March 10, 2021. USAID and the Ministry of Water and Irrigation convened 50 experts from Jordan’s water sector, the Ministry of Health, the National Center for Security and Crisis Management, funding agencies, and academia to discuss how to use wastewater surveillance data as a supplement to clinical data on COVID-19. A member of USAID/Jordan’s water team explains that “Wastewater surveillance can identify COVID-19 hotspots, provide early warning of new outbreaks, and confirm trends in clinical data’’.

The project also used these lessons to develop a “road map” for expanding Jordan’s surveillance system to cover everyone in the country who is served by sewers. The road map, which is part of the project report, emphasizes the need to define specific public health actions to be linked to the wastewater data.

National testing can complement clinical testing data and help allocate critical public health resources to manage the spread of COVID-19. And because many other human pathogens can be measured in wastewater, development of wastewater surveillance capacity in Jordan will also be helpful for management of outbreaks of diseases — both known and unknown — other than COVID-19.

By the Global Waters Communication and Knowledge Management Activity supported by USAID’s RFS Center for Water Security, Sanitation, and Hygiene



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USAID Water Team

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