A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data

As clinical specimens are collected and analyzed less for SARS-CoV-2, variant detection in wastewater provides a readily accessible and rich source of information on SARS-CoV-2 evolution. The detection of pathogen targets in wastewater samples using PCR assays is a sensitive, cost-effective way to monitor the levels of infectious diseases, like SARS-CoV-2, in a community. Unfortunately, because PCR-based methods are typically not used to distinguish between viral variants, most wastewater testing labs must rely on more expensive, time-consuming, and resource-intensive sequencing methods for these results. Building upon recent developments for variant detection using quantitative PCR, we developed and assessed a novel, customizable digital PCR-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more rapid, cost-effective, and accessible than sequencing. We characterize the method and offer insights for improvement in future implementations.