A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Authors

Nakamura, J., Miyazaki, K., Torii, S., Kitajima, M., Mikamo, K., Kimihira, T., Morimoto, L., Ashayqa, H., Ito, J., Takeshita, K., Kosugi, S., Minegishi, Y., Ito, M., Hirano, R., Ishida, S., Yoshimi, K., Halfmann, P. J., Kawaoka, Y., Mashimo, T.

Abstract

Rapidly converting viral genome information into deployable molecular tests remains a major challenge in outbreak preparedness. We developed CONAN-SWIFT (Simple Workflow for Isothermal Field Testing), a sequence-to-test platform that integrates computational assay design, reverse-transcription loop-mediated isothermal amplification, CRISPR-Cas3 detection, reagent lyophilization and lateral-flow readout. Sequence-guided assays for Andes virus and Bundibugyo virus were established within approximately three weeks and extended to four additional filoviruses. A web-based designer supported crRNA selection, and systematic RT-LAMP primer optimization improved amplification performance. Recombinant Escherichia coli-expressed Cascade enabled standardized preparation of lyophilized Cas3-detection reagents, which were combined with a battery-operated isothermal device. The portable system detected as few as 10 input RNA copies per reaction within approximately 40 min. It also detected viral RNA and biologically contained, replication-incompetent Ebola virus in spiked human blood and concentrated wastewater. These findings establish the analytical feasibility of a rapidly adaptable CRISPR-Cas3 engineering framework for decentralized detection of emerging RNA viruses.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 27 Aug 2026.

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