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 signal 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, is sensitive enough to detect viral loads of SARS-CoV-2 in a broad concentration range corresponding to a threshold cycle range of 16 to 39. Clinical specimens were tested at Kingston Health Sciences using a clinically validated PCR assay and variants were determined using whole genome sequencing.

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

“…Many recent studies have successfully developed POC devices that rely on the naked eye to interpret qualitative assay results [14,15] or complex read-out systems to analyze the assay [16,17]. Other recent studies have used a digital camera to evaluate the result of the assay, but rely on the sample being prepared in PCR tubes prior to amplification [6,18,19], or a complex and expensive amplification process such as the use of a centrifugal device, or droplet microfluidics [20,21]. As shown by [19], artificial intelligence (AI) can be used to augment the sensitivity and specificity of LAMP assays, but it requires images to train and classify features and patterns [19].…”