Surveillance of SARS-CoV-2 genomic variants in wastewater

Wastewater surveillance results are published weekly. They are available, along with further details about the project, on the covSPECTRUM dashboard, under external page 'Wastewater in Switzerland' story.

The genomic analysis of wastewater samples, aimed at the detection and relative quantification of SARS-CoV-2 variants, presents several new challenges. The samples contain a mixture of heterogeneous genetic material, which is often highly fragmented and present in low concentrations.

To address these issues, we have extended our external page V-pipe viral genomics workflow with newly developed tools. external page COJAC allows for the early detection of newly introduced variants, while external page LolliPop enables the quantification of relative abundances of variants and the tracking of their progression over time. We utilize these results to detect, track and model the competition between currently circulating SARS-CoV-2 variants, thereby providing valuable information for public health authorities.