Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems

Kayla G. Barnes (), Joshua I. Levy, Jillian Gauld, Jonathan Rigby, Oscar Kanjerwa, Christopher B. Uzzell, Chisomo Chilupsya, Catherine Anscombe, Christopher Tomkins-Tinch, Omar Mbeti, Edward Cairns, Herbert Thole, Shannon McSweeney, Marah G. Chibwana, Philip M. Ashton, Khuzwayo C. Jere, John Scott Meschke, Peter Diggle, Jennifer Cornick, Benjamin Chilima, Kondwani Jambo, Kristian G. Andersen, Gift Kawalazira, Steve Paterson, Tonney S. Nyirenda and Nicholas Feasey
Additional contact information
Kayla G. Barnes: Kamuzu University of Health Sciences
Joshua I. Levy: Liverpool School of Tropical Medicine
Jillian Gauld: The Scripps Research Institute
Jonathan Rigby: Kamuzu University of Health Sciences
Oscar Kanjerwa: Kamuzu University of Health Sciences
Christopher B. Uzzell: Liverpool School of Tropical Medicine
Chisomo Chilupsya: Kamuzu University of Health Sciences
Catherine Anscombe: Kamuzu University of Health Sciences
Christopher Tomkins-Tinch: Harvard TH Chan School of Public Health
Omar Mbeti: Harvard University
Edward Cairns: Blantyre District Health Office
Herbert Thole: Kamuzu University of Health Sciences
Shannon McSweeney: Kamuzu University of Health Sciences
Marah G. Chibwana: Kamuzu University of Health Sciences
Philip M. Ashton: Kamuzu University of Health Sciences
Khuzwayo C. Jere: Kamuzu University of Health Sciences
John Scott Meschke: University of Liverpool
Peter Diggle: University of Washington
Jennifer Cornick: Kamuzu University of Health Sciences
Benjamin Chilima: Lancaster University
Kondwani Jambo: Kamuzu University of Health Sciences
Kristian G. Andersen: Liverpool School of Tropical Medicine
Gift Kawalazira: Harvard University
Steve Paterson: Blantyre District Health Office
Tonney S. Nyirenda: Kamuzu University of Health Sciences
Nicholas Feasey: Kamuzu University of Health Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020–May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.

Date: 2023
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DOI: 10.1038/s41467-023-43047-y

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