Estimating relative abundance of two SARS-CoV-2 variants through wastewater surveillance at two large metropolitan sites

Abstract Monitoring SARS-CoV-2 variants of concern (VOCs) is critical for public health management of COVID-19. Case isolate sequencing is resource-intensive and not all isolates can be sequenced, and thus are not representative. However, since wastewater SARS-CoV-2 RNA concentrations correlate with COVID-19 case incidence in sewersheds, tracking VOCs through wastewater is appealing. We developed targeted digital RT-PCR assays to monitor abundance of select mutations in Alpha and Delta VOCs in wastewater settled solids, applied these to July 2020-August 2021 samples from two large metropolitan sewersheds, and compared results to estimates of variant abundance from case isolate sequencing. Wastewater measurements tracked closely with case isolate estimates at each site (rp= 0.82, 0.88 for Alpha and rp= 0.97 for Delta). Mutations were detected in wastewater measurements even at levels <5% of circulating virus and in samples available weeks before case isolate results. Therefore, wastewater variant monitoring should be strategically deployed to complement case isolate sequencing.