Sewage surveillance of SARS-CoV-2 in Tokyo (May 2020–June 2022): method using high-throughput, fully-automated platform

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is shed in saliva, sputum, and feces of the novel coronavirus disease 2019 (COVID-19) patients, and SARS-CoV-2 RNA has been detected in sewage. Thus, many regions worldwide have implemented the measurement of SARS-CoV-2 RNA in sewage as a monitoring tool for COVID-19 prevalence. Here, we report the monitoring of two wastewater treatment plants in Tokyo from May 2020 to June 2022 using a fully automated genetic testing method for the solid fraction of sewage. We found that SARS-CoV-2 sewage monitoring using the Panther System with the Aptima SARS-CoV-2 Assay Kit is an effective method of qualitative monitoring. Furthermore, spike gene mutations (N501Y, L452R, E484A) by real-time PCR using test residues were detected in some samples, which reflected the epidemic status. Nevertheless, our findings demonstrate that the use of a fully automated testing platform is effective for SARS-CoV-2 RNA detection in the solid fraction of sewage.