Rise and fall of SARS-CoV-2 variants in Rotterdam

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

Izquierdo-Lara, Ray W. (Erasmus MC)
Heijnen, Leo (KWR Water Research Institute)
Oude Munnink, Bas B. (Erasmus MC)
Schapendonk, Claudia M.E. (Erasmus MC)
Elsinga, Goffe (KWR Water Research Institute)
Langeveld, J.G. (TU Delft Sanitary Engineering; Partners4UrbanWater)
Post, Johan (Partners4UrbanWater)
Prasad, Divyae K. (Erasmus MC)
Medema, G.J. (TU Delft Sanitary Engineering; KWR Water Research Institute)

2023

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.

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

http://resolver.tudelft.nl/uuid:a67a9094-d0ac-40d7-b310-462e5f5043bd

https://doi.org/10.1016/j.scitotenv.2023.162209

2023-08-14

0048-9697

Science of the Total Environment, 873

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.

Institutional Repository

journal article

© 2023 Ray W. Izquierdo-Lara, Leo Heijnen, Bas B. Oude Munnink, Claudia M.E. Schapendonk, Goffe Elsinga, J.G. Langeveld, Johan Post, Divyae K. Prasad, G.J. Medema, More Authors