Wastewater-based epidemiology is now widely used as an indirect tool to monitor the
spread of SARS-CoV-2. In this study, five different sample matrices representing diverse
phases of the wastewater treatment process were collected during the second wave of
SARS-CoV-2 from two wastewater treatment plants (WWTPs) serving the Civil Hospital and
Sacca Fisola island in Venice, Italy. Positive SARS-CoV-2 detections occurred at both
WWTPs, and data on viral genome detection rate and quantification suggest that the
pellet (i.e., the particulate resulting from the influent) is a sensitive matrix that
permits reliable assessment of infection prevalence while reducing time to results. On
the contrary, analysis of post-treatment matrices provides evidence of the
decontamination efficacy of both WWTPs. Finally, direct sequencing of wastewater samples
enabled us to identify B.1.177 and B.1.160 as the prevalent SARS-CoV-2 lineages
circulating in Venice at the time of sampling. This study confirmed the suitability of
wastewater testing for studying SARS-CoV-2 circulation and established a simplified
workflow for the prompt detection and characterization of the virus.