The Korea Advanced Institute of Science and Technology (KAIST) and an international research team have developed a new diagnostic technology that simultaneously identifies various viruses and their variants by leveraging differences in the reaction speed of CRISPR gene-editing tools. The method is expected to shift the landscape of emerging infectious disease response by streamlining the traditionally complex testing process.
KAIST announced Wednesday that a research team led by Professor Sungmin Son of the Department of Bio and Brain Engineering developed the diagnostic technology using "Cas13," which targets ribonucleic acid (RNA), in collaboration with the University of California, Berkeley and the Gladstone Institutes.
At the core of the technology is the CRISPR protein Cas13. CRISPR proteins locate and cut specific genes, activating upon recognizing their target. Cas13, in particular, emits a fluorescent signal by cutting surrounding RNA once it finds its target RNA.
Existing technologies required different CRISPR proteins or fluorescent substances of various colors to detect multiple viruses simultaneously, resulting in complex structures that were difficult to apply in real-world settings.
The research team took a different approach, focusing on the fact that Cas13's "cutting" speed varies depending on the type of virus it binds to. Observing reactions at the single-molecule level inside tiny droplets, the team confirmed that each combination of guide RNA and target RNA produces a unique reaction-speed pattern. Guide RNA is an RNA molecule that serves as "location information," directing CRISPR proteins to the target they are meant to find.
By analyzing these patterns, the researchers developed a "kinetic barcoding" technology that reads reaction speeds like a barcode. This enables a single CRISPR protein to simultaneously distinguish among multiple viruses and variants.
Modifying the design of guide RNA also makes it possible to control the reaction speed of CRISPR cutting, theoretically allowing the method to be expanded to identify a greater number of viruses at once.
The testing process has also been simplified. While conventional methods required a "reverse transcription" step to convert RNA viruses into DNA for detection, the new technology can detect RNA directly. In clinical sample experiments, the team successfully distinguished various respiratory viruses and COVID-19 (SARS-CoV-2) variants accurately in a single test.
"This study is the first case of using a new type of information—the reaction speed of CRISPR proteins—for diagnostics, going beyond simply determining whether a virus is present," Professor Son said. "It will serve as a next-generation platform for diagnosing various infectious diseases that may emerge in the future, all at once and on site."
Professor Son of KAIST participated as the first author and co-corresponding author of the study, which was published last month on the 31st in the world-leading journal Nature Biomedical Engineering.
