Nonenzymatic Detection of SARS-CoV‑2 RNA Using DNA Nanoswitches

The emergence of a highly contagious coronavirus in 2019 led to an unprecedented need for large-scale diagnostic testing. The associated challenges, including reagent shortages, cost, deployment delays, and turnaround time, have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that can be read by gel electrophoresis. A multitargeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We applied our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This tool can benefit diagnostic options for COVID-19 and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe that this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.