Development and evaluation of a molecular assay for the detection and quantification of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus from municipal wastewater in British Columbia

Abstract

The ability to monitor the prevalence of respiratory viruses in a community depends on testing infrastructure, surveillance programs, and community engagement. Wastewater-based surveillance has recently evolved as a tool to monitor disease at a population level with reduced costs, diverse surveillance coverage, and inherently passive population participation. This study designed a molecular assay for the detection and quantification of multiple respiratory viruses—SARS-CoV-2, influenza A, influenza B, and Respiratory Syncytial Virus (RSV)—from wastewater samples. The presence of inhibitory substances in the wastewater matrix and multiple molecular targets did not prove to be limiting factors for the performance of the assay. Evaluation of the assay using municipal wastewater treatment plant samples showed a strong concordance with publicly available surveillance and clinical case data in British Columbia, Canada. Existing and future community testing programs for respiratory viruses should integrate wastewater-based surveillance to capture asymptomatic/non-testing populations, expand surveillance coverage, and provide greater insight into the community dynamics of respiratory viruses.