Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance

Ray W. Izquierdo-Lara, Leo Heijnen, Bas B. Oude Munnink, Claudia M.E. Schapendonk, Goffe Elsinga, Jeroen Langeveld, Johan Post, Divyae K. Prasad, Gertjan Medema, More Authors

Research output: Contribution to journalArticleScientificpeer-review

5 Citations (Scopus)
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Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.
Original languageEnglish
Article number162209
Number of pages11
JournalScience of the Total Environment
Publication statusPublished - 2023

Bibliographical note

Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.


  • Next generation sequencing
  • RT-ddPCR
  • SARS-CoV-2
  • Single nucleotide variant
  • Viral diversity
  • Wastewater genomic surveillance


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