A pan-European study of SARS-CoV-2 variants in wastewater under the EU Sewage Sentinel System

Agrawal, S.; Orschler, L.; Schubert, S.; Zachmann, K.; Heijnen, L.; Tavazzi, S.; Gawlik, B. M.; de Graaf, M.; Medema, G.; Lackner, S.

Wastewater based surveillance employing qPCR has already shown its utility for monitoring SARS-CoV-2 at community level, and consequently the European Commission has recommended the implementation of an EU Sewage Sentinel System. However, using sequencing for the determination of genomic variants in wastewater is not fully established yet. Therefore, we focused on the sequencing analysis of SARS-CoV-2 RNA in wastewater samples collected across 20 European countries including 54 municipalities. The results provide insight into the abundance and the profile of the mutations associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2, which were present in various wastewater samples. This study shows that integrating genomic and wastewater-based epidemiology (WBE) can support the identification of variants circulating in a city at community level.