Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing, the netherlands and belgium

Ray Izquierdo-Lara, Goffe Elsinga, Leo Heijnen, Bas B. Oude Munnink, Claudia M.E. Schapendonk, David Nieuwenhuijse, Matthijs Kon, Lu Lu, Frank Møller Aarestrup, Samantha Lycett, Gertjan Medema, Marion P.G. Koopmans, Miranda De Graaf*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

Original languageEnglish
JournalEmerging Infectious Diseases
Issue number5
Pages (from-to)1405-1415
Publication statusPublished - 2021

Bibliographical note

Funding Information:
This work was supported by the European Union’s Horizon H2020 grants VEO (grant no. 874735) and METASTAVA (grant no. 773830), the Erasmus MC foundation, and the Adessium Foundation.

Publisher Copyright:
© 2021 Centers for Disease Control and Prevention (CDC). All rights reserved.


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