Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.

The world is currently facing a serious health burden of waterborne diseases, including diarrhea, gastrointestinal diseases, and systemic illnesses. The control of these infectious diseases ultimately depends on the access to safe drinking water, properly managed sanitation, and hygiene practices. Therefore, ultrasensitive, rapid, and specific monitoring platforms for bacterial pathogens in ambient waters at the point of sample collection are urgently needed. We conducted a literature review on state-of-the-art research of rapid in-field aquatic bacteria detection methods, including cell-based methods, nucleic acid amplification detection methods, and biosensors. The detection performance, the advantages, and the disadvantages of the technologies are critically discussed. We envision that promising monitoring approaches should be automated, real-time, and target-multiplexed, thus allowing comprehensive evaluation of exposure risks attributable to waterborne pathogens and even emerging microbial contaminants such as antibiotic resistance genes, which leads to better protection of public health.

A proof-of-concept portable pathogen detection system was developed.• Microfluidic disc integrates a complete digital DNA amplification assay. • Sample-to-answer results are achieved within one hour in a single step. • On disc bacterial concentration is achieved through integration with adsorption beads.