Programmable low-cost DNA-based platform for viral RNA detection

Zhou, Lifeng; Chandrasekaran, Arun Richard; Punnoose, Jibin Abraham; Bonenfant, Gaston; Charles, Stephon; Levchenko, Oksana; Badu, Pheonah; Cavaliere, Cassandra; Pager, Cara T.; Halvorsen, Ken

Viral detection is critical for controlling disease spread and progression. Recent emerging threats including the Zika and Ebola virus outbreaks highlight the cost and difficulty in responding rapidly. In low-resource areas, a key obstacle is quick and accurate detection of viruses near the point of care. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches designed to mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show non-enzymatic detection of viral RNA to the attomole level, with selective and multiplexed detection between related viruses and viral strains. For clinical-level sensitivity in biological fluids, we paired the assay with a sample preparation step using either RNA extraction or isothermal pre-amplification. Our assay can be performed with minimal or no lab infrastructure, and is readily adaptable (with ∼24-hour development time) to detect other viruses. Given this versatility, we expect that further development and field implementation will improve our ability to detect emergent viral threats and ultimately limit their impact.