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

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. Importance Wastewater represents a pooled biological sample of the contributing community and thus a resource of assessing community health. Here we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.