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

Author

Listed:
  • Kayla G. Barnes

    (Kamuzu University of Health Sciences
    Harvard TH Chan School of Public Health
    Broad Institute of MIT and Harvard
    Liverpool School of Tropical Medicine)

  • Joshua I. Levy

    (Liverpool School of Tropical Medicine)

  • Jillian Gauld

    (The Scripps Research Institute)

  • Jonathan Rigby

    (Kamuzu University of Health Sciences
    Bill & Melinda Gates Foundation)

  • 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
    Bill & Melinda Gates Foundation)

  • Christopher Tomkins-Tinch

    (Harvard TH Chan School of Public Health
    Imperial College London)

  • Omar Mbeti

    (Harvard University)

  • Edward Cairns

    (Blantyre District Health Office)

  • Herbert Thole

    (Kamuzu University of Health Sciences)

  • Shannon McSweeney

    (Kamuzu University of Health Sciences
    Bill & Melinda Gates Foundation)

  • Marah G. Chibwana

    (Kamuzu University of Health Sciences)

  • Philip M. Ashton

    (Kamuzu University of Health Sciences
    Blantyre District Health Office)

  • Khuzwayo C. Jere

    (Kamuzu University of Health Sciences
    Blantyre District Health Office
    University of Liverpool)

  • John Scott Meschke

    (University of Liverpool)

  • Peter Diggle

    (University of Washington)

  • Jennifer Cornick

    (Kamuzu University of Health Sciences
    Blantyre District Health Office)

  • Benjamin Chilima

    (Lancaster University)

  • Kondwani Jambo

    (Kamuzu University of Health Sciences
    The Scripps Research Institute
    Public Health Institute of Malawi)

  • Kristian G. Andersen

    (Liverpool School of Tropical Medicine
    Scripps Research Translational Institute)

  • Gift Kawalazira

    (Harvard University)

  • Steve Paterson

    (Blantyre District Health Office)

  • Tonney S. Nyirenda

    (Kamuzu University of Health Sciences
    Kamuzu University of Health Sciences)

  • Nicholas Feasey

    (Kamuzu University of Health Sciences
    Bill & Melinda Gates Foundation
    University of St Andrews)

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.

Suggested Citation

  • 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 Ca, 2023. "Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43047-y
    DOI: 10.1038/s41467-023-43047-y
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