Programmable DNA nanoswitches can rapidly detect emerging viruses, including SARS-CoV-2

Programmable DNA nanoswitches that bind to viral RNA in human body fluids may provide an inexpensive platform to rapidly detect a wide variety of emerging viruses, including SARS-CoV-2, according to a new study.

This approach may make testing more manageable in resource-limited areas, since it does not require enzymes or significant laboratory infrastructure, only costs about 1 penny per reaction, and can be performed within hours. RNA viruses are often the culprits behind widespread outbreaks, since their high mutation rates enable them to evolve quickly.

Detecting these emergent RNA viruses remains challenging, especially in impoverished areas, since detection time windows can be as short as just a few days and laboratories may not be equipped to conduct immunoglobulin blood tests, which remain standard for clinical testing but sometimes lead to false positive results.

To help overcome these challenges, Zhou et al. developed DNA nanoswitches that bind to both ends of target viral RNAs, forming loop-shaped compounds.

These negatively-charged, RNA-containing nanoswitch loops are then placed in a gel and stimulated with an electrical current, pulling them towards a positive electrode on the other end of the gel. Since the nanoswitches move more slowly when they are bound to viral RNA, this gel electrophoresis technique reveals the virus' presence.

The researchers first tested this approach with DNA nanoswitches designed to target a sequence in the Zika virus genome and demonstrated its ability to detect clinically-relevant levels of Zika RNA in human urine. Zhou et al. next developed nanoswitches to target SARS-CoV-2 RNA in human saliva, finding that they could successfully detect the virus' presence within about 2 hours.

The nanoswitches also successfully differentiated between Zika virus and Dengue virus, which occur in overlapping geographical regions and cause similar symptoms, demonstrating the nanoswitches' potential to avoid misdiagnoses.