IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-41369-5.html
   My bibliography  Save this article

SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses

Author

Listed:
  • Mukhlid Yousif

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Said Rachida

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Setshaba Taukobong

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Nkosenhle Ndlovu

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Chinwe Iwu-Jaja

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Wayne Howard

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Shelina Moonsamy

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Nompilo Mhlambi

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Sipho Gwala

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Joshua I. Levy

    (The Scripps Research Institute)

  • Kristian G. Andersen

    (The Scripps Research Institute)

  • Cathrine Scheepers

    (University of the Witwatersrand)

  • Anne Gottberg

    (Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Nicole Wolter

    (Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Jinal N. Bhiman

    (Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Daniel Gyamfi Amoako

    (Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service)

  • Arshad Ismail

    (Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of Venda)

  • Melinda Suchard

    (University of the Witwatersrand)

  • Kerrigan McCarthy

    (Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
    University of the Witwatersrand)

Abstract

As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41369-5
    DOI: 10.1038/s41467-023-41369-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-41369-5
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-41369-5?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. 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.
    2. 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. 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.
    2. 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.
    3. 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.
    4. Denis Mongin & Nils Bürgisser & Gustavo Laurie & Guillaume Schimmel & Diem-Lan Vu & Stephane Cullati & Delphine Sophie Courvoisier, 2023. "Effect of SARS-CoV-2 prior infection and mRNA vaccination on contagiousness and susceptibility to infection," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. 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.

    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_s41467-023-41369-5. 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.