Enabling SARS-CoV-2 Wastewater Surveillance Using an Integrated Microfluidic Chip

Wastewater-based epidemiology (WBE) has emerged as a critical public health tool, offering cost-effective and noninvasive surveillance of infectious diseases through wastewater testing. Despite its potential, WBE implementation in low-resource settings is hindered by infrastructure limitations, lack of technical expertise, and dependence on centralized laboratories. This study presents a novel concentration-extraction-identification device (CEID), a point-of-use platform that integrates nucleic acid concentration, extraction, and detection into an affordable and user-friendly chip. The CEID employs immiscible filtration assisted by surface tension (IFAST) for nucleic acid extraction and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) for pathogen detection. Key parameters of the CEID were characterized and optimized, resulting in efficient nucleic acid extraction with minimal carry-over of inhibitory molecules. The performance was validated using SARS-CoV-2 spiked wastewater samples, achieving a detection limit of 113 Cp/mL. The CEID was further validated through a 6-week surveillance study, successfully detecting SARS-CoV-2 in wastewater from two locations with a high correlation to standard WBE methods and RT-qPCR. Costing approximately $11 per sample and requiring minimal hands-on time, the CEID demonstrates significant advantages in affordability, simplicity, and adaptability for rural and underserved regions. This technology offers a scalable solution to democratize WBE, enhancing global infectious disease surveillance and response, particularly in low- and middle-income countries.