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

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, Cathrine Scheepers, Anne Gottberg, Nicole Wolter, Jinal N. Bhiman, Daniel Gyamfi Amoako, Arshad Ismail, Melinda Suchard and Kerrigan McCarthy
Additional contact information
Mukhlid Yousif: Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
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
Nicole Wolter: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
Jinal N. Bhiman: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service
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
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

Nature Communications, 2023, vol. 14, issue 1, 1-9

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-41369-5

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