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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
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    References listed on IDEAS

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    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.
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    1. Braden T. Tierney & Jonathan Foox & Krista A. Ryon & Daniel Butler & Namita Damle & Benjamin G. Young & Christopher Mozsary & Kristina M. Babler & Xue Yin & Yamina Carattini & David Andrews & Alexande, 2024. "Towards geospatially-resolved public-health surveillance via wastewater sequencing," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. 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.

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