Accurate detection of pathogenic nucleic acids is crucial for early diagnosis, effective treatment, and containment of infectious diseases. It facilitates the timely identification of pathogens, aids in monitoring disease outbreaks, and helps prevent the spread of infections within healthcare settings and communities. We developed a multi-layered, paper-based microfluidic and miniaturized electrophoresis system for rapid nucleic acid extraction, separation, amplification, and detection, designed for resource-limited settings. Constructed from acrylic, transparency film, pressure-sensitive adhesion, and Whatman paper using a CO2 laser, the setup simplifies traditional methods and eliminates the need for complex equipment. DNA extraction and purification are achieved using Zweifach–Fung bifurcation and Fahraeus effect principles, with detection via a hydrogel-assisted colorimetric isothermal reverse transcriptase-loop-mediated isothermal amplification technique. The system accurately identified the SARS-CoV-2 N-gene and β-actin human gene, validated by a compact electrophoresis setup. In clinical validation with 12 patient specimens, the system demonstrated a positive predictive agreement of 83.0% and a negative predictive agreement of 100%. The system achieves a limit of detection of 1 copy/μl and can potentially transform nucleic acid detection assays in healthcare settings. This study addresses key challenges in nucleic acid detection, such as ensuring sample quality and quantity, reducing reliance on sophisticated equipment, preventing contamination, simplifying procedures, and providing rapid and accurate diagnostics for emerging pathogens.
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