Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron.

Tracking SARS-CoV-2 variants in wastewater is primarily performed by detecting characteristic mutations of the variants. Unlike the Delta variant, the emergence of the Omicron variant and its sublineages as variants of concern has posed a challenge in using characteristic mutations for wastewater surveillance. In this study, we monitored the temporal and spatial variation of SARS-CoV-2 variants by including all the detected mutations and compared whether limiting the analyses to characteristic mutations for variants like Omicron impact the outcomes. We collected 24-hour composite samples from 15 wastewater treatment plants (WWTP) in Hesse and sequenced 164 wastewater samples with a targeted sequencing approach from September 2021 to March 2022. Our results show that comparing the number of all the mutations against the number of the characteristic mutations reveals a different outcome. A different temporal variation was observed for the ORF1a and S gene. As Omicron became dominant, we observed an increase in the overall number of mutations. Based on the characteristic mutations of the SARS-CoV-2 variants, a decreasing trend for the number of ORF1a and S gene mutations was noticed, though the number of known characteristic mutations in both genes is higher in Omicron than Delta.

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.