Novel Digital PCR-based Workflow for SARS-CoV-2 Variant Detection in Wastewater: Performance Comparison with Whole-Genome Sequencing

Caryn Tyler
Aug 19
1 min read

Wastewater surveillance is a critical tool for monitoring infectious diseases like COVID-19 at the community level.¹ As the virus evolves, with variants differing in transmissibility and virulence, tracking these changes is vital for public health. While quantitative PCR is the gold standard for detection and quantification, it typically can’t differentiate among many variants. In contrast, whole-genome sequencing (WGS) provides comprehensive data but is often too complex and resource-intensive for routine wastewater testing.²

To address this, we developed a customizable digital PCR (dPCR)-based genotyping method for detecting SARS-CoV-2 variants in wastewater.³ This approach enables rapid, cost-effective screening for specific mutations, capturing both known and emerging variants.

We compared dPCR genotyping to WGS using the same elution from each sample and applied the method to wastewater collected across Illinois (Oct 2023–Apr 2024). Results showed high concordance between the two methods. dPCR data aligned with clinical trends and detected early signals of variant rise and decline in near real-time, highlighting its potential as a scalable and timely tool for community-level variant tracking.