CRISPR-Based Test Identifies Multiple Respiratory Viruses Simultaneously

Respiratory virus co-circulation complicates differential diagnosis, as overlapping symptoms can obscure etiology. Multiplex testing typically depends on multiple enzymes or fluorophores and multistep workflows that burden clinical laboratories. Faster, simpler methods that can detect several RNA viruses in a single reaction would improve throughput and triage. Now, a novel diagnostic technology enables simultaneous identification of multiple viruses and variants by measuring the reaction speed of CRISPR gene scissors.

Korea Advanced Institute of Science and Technology (KAIST), with collaborators at the University of California, Berkeley, and the Gladstone Institutes, have developed an RNA diagnostic approach termed kinetic barcoding. The system uses the CRISPR-based protein called Cas13, which becomes activated upon target recognition and then cleaves surrounding RNA to generate a fluorescent signal. By differentiating targets based on cleavage speed, the method eliminates the need for multiple nucleases typically required by existing CRISPR-based technologies.

At the single-molecule level inside microdroplets, distinct reaction-speed patterns arise for each guide RNA and target RNA combination, enabling barcode-like classification. Guide RNA is an RNA molecule that directs the gene-editing system to a specific target by providing the necessary positional information. The researchers tuned these kinetics by modifying guide RNA design, allowing scalable, simultaneous detection across a wide range of viruses. Because Cas13 directly interrogates RNA, the workflow omits reverse transcription, reducing steps compared with conventional approaches.

In testing on actual clinical samples, the approach distinguished multiple respiratory viruses and SARS‑CoV‑2 variants within a single reaction. The researchers note that using a single type of nuclease to resolve multiple infections reduces system complexity while maintaining multiplex capability. The work was published on March 31, 2026, in Nature Biomedical Engineering under the title “Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.”

“This study goes beyond simply determining whether a virus is present, and is the first case to use the reaction speed of gene scissors as a new form of diagnostic information. It will become a next-generation platform capable of diagnosing various infectious diseases at once in the field,” said Professor Sungmin Son, Department of Bio and Brain Engineering, KAIST.

Related Links
KAIST