Fig. 3: Concordant estimation of the selection advantage of Omicron BA.1 in Switzerland using clinical and wastewater-derived data.

A Map of Switzerland indicating the location of all six wastewater treatment plants (WWTPs) sampled in this study. The discs are scaled to represent the number of inhabitants in the respective sewersheds. B Log10 SARS-CoV-2 genome copies (gc) in wastewater (7-day rolling median) per new confirmed case in the sewersheds (7-day rolling median), throughout the spread of BA.1. The point colors represent the WWTP, and the solid line is a robust linear fit along with 95% confidence bands, showing an average reduction of gc / new case of 47% during the study period. C Progression of the Omicron BA.1 variant in Switzerland. Points represent average frequencies of the variant in different locations, estimated from clinical sequences (n = 8525, red) or wastewater (n = 280, blue) NGS samples. Solid lines represent logistic fits along with 95% Wald confidence bands. D Selection advantage estimates for BA.1 in the six WWTP regions (colors), based on wastewater NGS (n = 280, left) as well as wastewater ddPCR duplex assays targeting the S:HV69-70 deletion (n = 79, center) and S:L452R substitution (n = 74, right), compared with estimates derived from clinical sequencing from the cantons surrounding the WWTPs. Points represent maximum likelihood estimates, and error bars represent 95% Wald confidence intervals adjusted for overdispersion. The dashed lines represent the 1:1 relationship.