Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities

For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.

AGRAWAL Shelesh;  ORSCHLER Laura;  SCHUBERT Selina;  ZACHMANN Kira;  HEIJNEN Leo;  TAVAZZI Simona;  GAWLIK Bernd;  DE GRAAF Miranda;  MEDEMA Gertjan;  LACKNER Susanne; 

2022-02-22

PERGAMON-ELSEVIER SCIENCE LTD

JRC125637

0043-1354 (online),   

https://www.sciencedirect.com/science/article/pii/S0043135422001257,    https://publications.jrc.ec.europa.eu/repository/handle/JRC125637,   

10.1016/j.watres.2022.118162 (online),