A magnetic modulation biosensing-based molecular assay for rapid and highly sensitive clinical diagnosis of COVID-19

Margulis, Michael; Erster, Oran; Roth, Shira; Mandelboim, Michal; Danielli, Amos

Rapid and sensitive detection of human pathogens, such as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is an urgent and challenging task for clinical laboratories. Currently, the gold standard test for SARS-CoV-2-specific ribonucleic acid (RNA) is based on reverse transcription quantitative polymerase chain reaction (RT-qPCR), which relies on target amplification by Taq polymerase and uses a fluorescent resonance energy transfer (FRET)-based hydrolysis probe. Although this method is accurate and specific, it is also time consuming. To rapidly detect the presence of the viral RNA in clinical samples, we describe a new molecular assay that combines a highly sensitive magnetic modulation biosensing (MMB) system, rapid thermal cycling, and a modified double-quenched hydrolysis probe. Using in vitro transcribed SARS-CoV-2 RNA targets spiked in PCR-grade water, we found that the calculated limit of detection of the MMB-based molecular assay was 1.6 copies per reaction. Testing 309 RNA extracts from 170 confirmed RT-qPCR SARS-CoV-2-negative individuals (30 of which are positive to other respiratory viruses) and 139 RT-qPCR SARS-CoV-2-positive patients ([Formula: see text]) resulted in 97.8% sensitivity, 100% specificity, and 0% cross-reactivity. The total turnaround time of the MMB-based assay is 30 minutes, which is 3–4 times faster than a standard RT-qPCR. By adjusting the primers and the probe set, the platform can be easily adapted to detect most of the pathogens that are currently being diagnosed by RT-qPCR.