A Miniaturized System for Rapid, Isothermal Detection of SARS-CoV-2 in Human and Environmental Samples

Abstract

We report a small-footprint cost-effective isothermal rapid DNA amplification system, with integrated microfluidics for automated sample analysis and detection of SARS-CoV-2 in human and environmental samples. Our system measures low-level fluorescent signals in real-time during amplification, while maintaining the desired assay temperature on a low power, portable system footprint. A unique soft microfluidic chip design was implemented to mitigate thermocapillary effects and facilitate optical alignment for automated image capture and signal analysis. The system-on-board prototype, coupled with the LAMP primers designed by BioCoS, was sensitive enough to detect large variations in viral loads of SARS-CoV-2 corresponding to a threshold cycle range of 16 to 39. Furthermore, tested samples consisted of a broad range of viral strains and lineages identified in Canada during 2021–2022. Clinical specimens were collected and tested at the Kingston Health Science Centre using a clinically validated PCR assay, and variants were determined using whole genome sequencing.

Keywords

• loop-mediated isothermal amplification
• soft microfluidic chip
• severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)
• system on board integration