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

Highlights

• Going beyond measuring the total SARS-CoV-2 RNA concentration in wastewater.

• Integrating genome sequencing to wastewater-based epidemiology.

• Approach to obtain high-quality and full coverage of SARS-CoV-2 genome.

• The genome sequencing method used worked for all wastewater samples.

• Diversity of SARS-CoV-2 VOCs in 54 European municipalities revealed through genome sequencing of wastewater samples.

Abstract

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.