Fig. 4: Prevalence and fitness advantage estimation for Zurich based on wastewater and clinical sequencing data.
From: Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC
a, Top: Alpha (B.1.1.7) prevalence estimates based on wastewater sequencing data and on cantonal clinical sequencing data for Zurich. Bottom: frequencies of Alpha-characteristic substitutions found in wastewater sequencing samples, which are aggregated and smoothed in the top panel. Grey columns show dates without wastewater samples. White columns show dates of failed experiments (insufficient coverage/no SARS-CoV-2 RNA detected in the sample). Orange and red bars indicate the frequency of Alpha-positive cantonal clinical samples, which are also smoothed. The red parts indicate the fraction of Alpha-positive samples that were sequenced retrospectively in March/April 2021 (cut-off date for the GISAID submission date, 21 March 2021). Solid lines represent the smoothed estimates and shaded areas represent 95% confidence bands. b, Estimates of the transmission fitness advantage fd, computed online (Methods) using the wastewater (blue), cantonal clinical (orange) and city clinical (green) sequencing data only until the respective timepoints for Zurich. Solid lines represent the maximum likelihood estimates, shaded areas represent 95% confidence intervals and the horizontal black line indicates offline estimate of fd based on clinical samples of the Greater Zurich Area dated 14 December 2020 to 11 February 2021 from Chen et al.19.
