Detection of SARS-CoV-2 variant Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in wastewater settled solids using mutation-specific assays is associated with regional detection of variants in clinical samples (preprint)

Changes in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive relative to other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital RT-PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in wastewater settled solids samples collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic to each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate to regional estimates of the proportion of clinical infections caused by each VOC. These results suggest targeted RT-PCR assays can be used to detect variants circulating in communities and inform public health response to the pandemic.

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

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.