How sewage can help countries get ahead of COVID-19 variants

August 11, 2022 by Deborah Oroszlan

In places with limited testing capacity, environmental surveillance of sewage and surface water may offer early warnings of outbreaks.

Environment and Public Health Organization staff and volunteer in Katmandu, Nepal, taking wastewater and sludge samples. Photo: PATH/S. Dahal.

Environment and Public Health Organization staff and volunteer in Katmandu, Nepal, taking wastewater and sludge samples. Photo: PATH/S. Dahal.

Editor’s note: A version of this article was originally published on October 12, 2021. It has been updated to include information about the costs and cost-effectiveness of conducting environmental surveillance for SARS-CoV-2.

When viruses are shed in feces, public health programs can assess viral presence in communal wastewater to determine local trends in disease prevalence. Environmental surveillance of sewage systems, fecal sludge, and impacted surface water is already used to monitor communities for infectious diseases such as polio.

With SARS-CoV-2 shed in feces by the symptomatic and asymptomatic alike, environmental surveillance (also called wastewater-based epidemiology) could be a powerful tool to help countries and health systems control COVID-19—especially countries and health systems with limited capacity to perform clinical testing and contact tracing. Because virus “shedding” begins soon after infection, sewage and wastewater provides a real-time view of trends in community infection.

As a complement to clinical testing, environmental surveillance can quickly provide insights into the circulation of SARS-CoV-2, potentially predicting peaks and identifying newly imported variants.

The central challenge of environmental surveillance comes down to data interpretation. Right now, surveillance data interpretations can vary widely and there is minimal guidance on how to interpret and integrate the analyses into public health systems.

In-country collection, global support

To address these challenges head on, PATH is partnering with local organizations and institutions to launch in-country data collection pilots, and connecting those pilots to the Wastewater SPHERE data center (W-SPHERE) to encourage data sharing and interpretation.

A research collaboration of Michigan State University, KWR Water Research Institute, UC Merced, and Venthic Technologies, W-SPHERE applies data visualization tools to show sampling locations, presence of SARS-COV-2 and trends over time. These data sets are publicly available and accessible to researchers conducting analyses on methods for detecting the presence of SARS-CoV-2 and modeling studies to predict the prevalence of COVID-19 infections.

W-SPHERE also highlights how environmental surveillance data have been used to guide public health decision-making. Though most current examples come from high-income countries like the Netherlands, the hope is that other countries can draw on these illustrations to better use their own environmental surveillance data for public health decision-making.

“We’re really excited about this collaboration and its potential to inform COVID-19 response,” says Vajra Allan, program manager, PATH Diagnostics. “We’ve launched data collection pilots in Indonesia, Malawi, Nepal, and Pakistan. And the research teams are partnering closely with in-country leadership to develop long-term sustainability plans.”

In Blantyre, Malawi, the PATH-supported pilot is being implemented by Malawi Liverpool Wellcome Trust (MLW). They are conducting traditional wastewater surveillance using PCR and have started successfully sequencing wastewater samples.

"Over the past 18 months, we have seen that environmental surveillance detection can provide up to a week early warning prior to an increase in clinical cases,” says MLW Research Fellow Kayla Barnes, PhD. “Sequencing may provide even earlier detection. We recently identified the introduction of the Delta variant in Blantyre in samples collected about two weeks before it was detected it in hospitalized patients with SARS-CoV-2."

Sharing knowledge, evaluating affordability

In addition to supporting the collection and analysis of environmental surveillance samples, PATH has also established the COVID-19 Environmental Surveillance Technical Assistance Committee and the COVID-19 Environmental Surveillance Working Group—two bodies designed to facilitate collaboration and knowledge sharing between sites and key stakeholders.

The Technical Assistance Committee is composed of experts in environmental surveillance, epidemiology, and virology, the committee provides independent scientific review and technical assistance to researchers. The Working Group includes researchers from 11 different countries—each piloting or scaling up wastewater surveillance programs.

“The technical assistance committee and working group are crucial aspects of this work,” says Vajra. “These bodies allow us share knowledge and experience among environmental surveillance experts, public health practitioners and researchers in low- and middle-income countries. Together, we’re equipping decision-makers with data to inform public health measures while strengthening technical capacities at the same time.”

In addition to sample collection and analysis, PATH also evaluated the cost-effectiveness of conducting environmental surveillance using data from sites in Malawi and Nepal. Costing analysis showed that consumable and human resource costs resulted in the highest share. Cost per sample was higher in Kathmandu than in Blantyre, but when correlated per person in the catchment area and per year, costs were similar ranging from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu.

“This study has determined that environmental surveillance is not only a cost-saving measure, but it also helps to flatten the curve of transmission. This is especially valuable where clinical testing is not widely available and can help health systems and policymakers implement public health measures before a peak,” says Sophie Magnet PhD, Senior Technical Advisor, PATH Diagnostics and Epidemic Preparedness and Response.

Learn more about PATH Diagnostics

Program partners

Thank you to the many partners around the world supporting this work. Without your support, innovative programs like these would not be possible.

  • Environment and Public Health Organization (Nepal)
  • Institute for Disease Modeling (US)
  • KWR Water Research Institute (Netherlands)
  • Liverpool School of Tropical Medicine (UK)
  • Malawi-Liverpool-Wellcome Trust Clinical Research Programme (Malawi)
  • Michigan State University (US)
  • Murdoch Children’s Research Institute (Australia)
  • The Aga Khan University (Pakistan)
  • Tribhuvan University (Nepal)
  • Tulane University (US)
  • Universitas Gadjah Mada (Indonesia)
  • University of California, Merced (US)
  • University of Washington (US)
  • Venthic Technologies (Greece)
  • Yale University (US)