Tracking SARS-CoV-2 Variants in Georgia Wastewater Using dPCR: A One-Year Study and Comparison with Clinical Sample Genotyping and GISAID Sequencing

Caryn Tyler
Jun 12
1 min read

Wastewater surveillance has become a vital tool for monitoring infectious diseases like COVID-19 at the community level.(1) As microbes continue to mutate, giving rise to variants with differing transmissibility and virulence, tracking the emergence and prevalence of these variants has become a critical component of wastewater-based monitoring. Although PCR-based methods are the gold standard for pathogen detection and quantification, they are generally not designed to distinguish among a broad range of variants. Meanwhile, genomic sequencing—while comprehensive—is often too complex, time-consuming, and resource-intensive for many wastewater testing laboratories.(2)

In this study, we developed a customizable digital PCR (dPCR)-based genotyping approach to detect SARS-CoV-2 variants in wastewater.3 This method provides a rapid and cost-effective way to screen for specific variants, enabling detection of both known and emerging variants beyond predefined markers. We also built a streamlined data analysis pipeline and integrated the results into a public-facing dashboard to deliver real-time insights alongside clinical and GISAID sequencing data. Results from a year-long surveillance effort across Georgia (April 2023–April 2024) highlight the potential of wastewater-based dPCR genotyping as a scalable, timely, and community-representative approach for tracking SARS-CoV-2 variants.