Wastewater-based epidemiology (WBE) is a powerful tool to monitor consumption of chemical agents or exposure to pathogens within a given population. Historically, it has been used to track diseases such as measles, polio, and Hepatitis A. Since the advent of COVID-19, several countries have started using WBE as an early warning system for increasing SARS-CoV-2 infections. An interdisciplinary team at the South African Medical Research Council is doing just that by weekly sampling of 70 wastewater treatment plants from across South Africa and determining the SARS-CoV-2 copies/ml in present in each treatment plant. As new variants of concern (VOC) are identified clinically, our team monitors each treatment plant for their emergence using PCR-based methods. In addition to this, we use sequence the genomes of SARS-CoV-2 from each treatment plant using ATOPlex technology from MGI. We show the utility of using WBE to predict increasing SARS-CoV-2 infection rates in communities as well as an early detection of system for the emergence of variants of concern.

*Unless otherwise informed, all sequencers and sequencing reagents are not available in Germany, USA, Spain, UK, Hong Kong, Sweden, Belgium, and Italy.