Microchip RT-PCR Detection of Nasopharyngeal SARS-CoV-2 Samples

Abstract Fast, accurate and reliable diagnostic tests are critical for controlling the spread of the 2019 Coronavirus disease associated with SARS-CoV-2 infection. The current gold standard for testing is real time PCR (RT-PCR), however, during the current pandemic, supplies of testing kits and reagents have been limited. We report the validation of a rapid (30 min), user-friendly and accurate microchip RT-PCR assay for detection of SARS-CoV-2 from nasopharyngeal swab RNA extracts. Microchips pre-loaded with COVID-19 primers and probes for the N gene accommodate 1.2 μl reaction volumes, lowering the required reagents by 10-fold compared to tube-based RT-PCR. We validated our assay using contrived reference samples and 21 clinical samples from patients in Canada, determining a limit of detection of 1 copy per reaction. The microchip RT-PCR provides a significantly lower resource alternative to the CDC approved real-time RT-PCR assays with comparable sensitivity, showing 100% positive and negative predictive agreement of clinical samples.