IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43047-y.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43047-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-43047-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Roman Wölfel & Victor M. Corman & Wolfgang Guggemos & Michael Seilmaier & Sabine Zange & Marcel A. Müller & Daniela Niemeyer & Terry C. Jones & Patrick Vollmar & Camilla Rothe & Michael Hoelscher & To, 2020. "Author Correction: Virological assessment of hospitalized patients with COVID-2019," Nature, Nature, vol. 588(7839), pages 35-35, December.
    2. Davida S. Smyth & Monica Trujillo & Devon A. Gregory & Kristen Cheung & Anna Gao & Maddie Graham & Yue Guan & Caitlyn Guldenpfennig & Irene Hoxie & Sherin Kannoly & Nanami Kubota & Terri D. Lyddon & M, 2022. "Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Nicolae Sapoval & Yunxi Liu & Esther G. Lou & Loren Hopkins & Katherine B. Ensor & Rebecca Schneider & Lauren B. Stadler & Todd J. Treangen, 2023. "Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    4. Raquel Viana & Sikhulile Moyo & Daniel G. Amoako & Houriiyah Tegally & Cathrine Scheepers & Christian L. Althaus & Ugochukwu J. Anyaneji & Phillip A. Bester & Maciej F. Boni & Mohammed Chand & Wonderf, 2022. "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa," Nature, Nature, vol. 603(7902), pages 679-686, March.
    5. Houriiyah Tegally & Eduan Wilkinson & Marta Giovanetti & Arash Iranzadeh & Vagner Fonseca & Jennifer Giandhari & Deelan Doolabh & Sureshnee Pillay & Emmanuel James San & Nokukhanya Msomi & Koleka Mlis, 2021. "Detection of a SARS-CoV-2 variant of concern in South Africa," Nature, Nature, vol. 592(7854), pages 438-443, April.
    6. Tafadzwa Dzinamarira & Grant Murewanhema & Patrick Gad Iradukunda & Roda Madziva & Helena Herrera & Diego F. Cuadros & Nigel Tungwarara & Itai Chitungo & Godfrey Musuka, 2022. "Utilization of SARS-CoV-2 Wastewater Surveillance in Africa—A Rapid Review," IJERPH, MDPI, vol. 19(2), pages 1-10, January.
    7. Smruthi Karthikeyan & Joshua I. Levy & Peter Hoff & Greg Humphrey & Amanda Birmingham & Kristen Jepsen & Sawyer Farmer & Helena M. Tubb & Tommy Valles & Caitlin E. Tribelhorn & Rebecca Tsai & Stefan A, 2022. "Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission," Nature, Nature, vol. 609(7925), pages 101-108, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yunxi Liu & Nicolae Sapoval & Pilar Gallego-García & Laura Tomás & David Posada & Todd J. Treangen & Lauren B. Stadler, 2024. "Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. X. Tong & R. P. McNamara & M. J. Avendaño & E. F. Serrano & T. García-Salum & C. Pardo-Roa & H. L. Bertera & T. M. Chicz & J. Levican & E. Poblete & E. Salinas & A. Muñoz & A. Riquelme & G. Alter & R., 2023. "Waning and boosting of antibody Fc-effector functions upon SARS-CoV-2 vaccination," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Mukhlid Yousif & Said Rachida & Setshaba Taukobong & Nkosenhle Ndlovu & Chinwe Iwu-Jaja & Wayne Howard & Shelina Moonsamy & Nompilo Mhlambi & Sipho Gwala & Joshua I. Levy & Kristian G. Andersen & Cath, 2023. "SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    4. Dapeng Li & David R. Martinez & Alexandra Schäfer & Haiyan Chen & Maggie Barr & Laura L. Sutherland & Esther Lee & Robert Parks & Dieter Mielke & Whitney Edwards & Amanda Newman & Kevin W. Bock & Mahn, 2022. "Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Meriem Bekliz & Kenneth Adea & Pauline Vetter & Christiane S. Eberhardt & Krisztina Hosszu-Fellous & Diem-Lan Vu & Olha Puhach & Manel Essaidi-Laziosi & Sophie Waldvogel-Abramowski & Caroline Stephan , 2022. "Neutralization capacity of antibodies elicited through homologous or heterologous infection or vaccination against SARS-CoV-2 VOCs," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    6. Claudia Del Vecchio & Bethan Cracknell Daniels & Giuseppina Brancaccio & Alessandra Rosalba Brazzale & Enrico Lavezzo & Constanze Ciavarella & Francesco Onelia & Elisa Franchin & Laura Manuto & Federi, 2022. "Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    7. Cathrine Scheepers & Josie Everatt & Daniel G. Amoako & Houriiyah Tegally & Constantinos Kurt Wibmer & Anele Mnguni & Arshad Ismail & Boitshoko Mahlangu & Bronwen E. Lambson & Darren P. Martin & Eduan, 2022. "Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    8. Judith U. Oguzie & Brittany A. Petros & Paul E. Oluniyi & Samar B. Mehta & Philomena E. Eromon & Parvathy Nair & Opeoluwa Adewale-Fasoro & Peace Damilola Ifoga & Ikponmwosa Odia & Andrzej Pastusiak & , 2023. "Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    9. Michael Tisza & Sara Javornik Cregeen & Vasanthi Avadhanula & Ping Zhang & Tulin Ayvaz & Karen Feliz & Kristi L. Hoffman & Justin R. Clark & Austen Terwilliger & Matthew C. Ross & Juwan Cormier & Hann, 2023. "Wastewater sequencing reveals community and variant dynamics of the collective human virome," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    10. Oliver Eales & Leonardo Oliveira Martins & Andrew J. Page & Haowei Wang & Barbara Bodinier & David Tang & David Haw & Jakob Jonnerby & Christina Atchison & Deborah Ashby & Wendy Barclay & Graham Taylo, 2022. "Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    11. Tobias Schlager & Ashley V. Whillans, 2022. "People underestimate the probability of contracting the coronavirus from friends," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-11, December.
    12. Alvin X. Han & Emma Hannay & Sergio Carmona & Bill Rodriguez & Brooke E. Nichols & Colin A. Russell, 2023. "Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    13. Joseph Pateras & Preetam Ghosh, 2022. "A Computational Framework for Exploring SARS-CoV-2 Pharmacodynamic Dose and Timing Regimes," Mathematics, MDPI, vol. 10(20), pages 1-12, October.
    14. Li Wang & Markus H. Kainulainen & Nannan Jiang & Han Di & Gaston Bonenfant & Lisa Mills & Michael Currier & Punya Shrivastava-Ranjan & Brenda M. Calderon & Mili Sheth & Brian R. Mann & Jaber Hossain &, 2022. "Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    15. Joseph A. Lewnard & Vennis Hong & Jeniffer S. Kim & Sally F. Shaw & Bruno Lewin & Harpreet Takhar & Sara Y. Tartof, 2023. "Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    16. Marta Baselga & Juan J. Alba & Alberto J. Schuhmacher, 2022. "The Control of Metabolic CO 2 in Public Transport as a Strategy to Reduce the Transmission of Respiratory Infectious Diseases," IJERPH, MDPI, vol. 19(11), pages 1-19, May.
    17. Mitchell D. Ramuta & Christina M. Newman & Savannah F. Brakefield & Miranda R. Stauss & Roger W. Wiseman & Amanda Kita-Yarbro & Eli J. O’Connor & Neeti Dahal & Ailam Lim & Keith P. Poulsen & Nasia Saf, 2022. "SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    18. Lisa Cariani & Beatrice Silvia Orena & Federico Ambrogi & Simone Gambazza & Anna Maraschini & Antonella Dodaro & Massimo Oggioni & Annarosa Orlandi & Alessia Pirrone & Sara Uceda Renteria & Mara Berna, 2020. "Time Length of Negativization and Cycle Threshold Values in 182 Healthcare Workers with Covid-19 in Milan, Italy: An Observational Cohort Study," IJERPH, MDPI, vol. 17(15), pages 1-10, July.
    19. Susanna Esposito & Federico Marchetti & Marcello Lanari & Fabio Caramelli & Alessandro De Fanti & Gianluca Vergine & Lorenzo Iughetti & Martina Fornaro & Agnese Suppiej & Stefano Zona & Andrea Pession, 2021. "COVID-19 Management in the Pediatric Age: Consensus Document of the COVID-19 Working Group in Paediatrics of the Emilia-Romagna Region (RE-CO-Ped), Italy," IJERPH, MDPI, vol. 18(8), pages 1-29, April.
    20. Ramon Roozendaal & Laura Solforosi & Daniel J. Stieh & Jan Serroyen & Roel Straetemans & Anna Dari & Muriel Boulton & Frank Wegmann & Sietske K. Rosendahl Huber & Joan E. M. van der Lubbe & Jenny Hend, 2021. "SARS-CoV-2 binding and neutralizing antibody levels after Ad26.COV2.S vaccination predict durable protection in rhesus macaques," Nature Communications, Nature, vol. 12(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43047-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.