CRISPR-Cas13a SHERLOCK assay for rapid and sensitive detection of chikungunya virus
Issued Date
2026-02-03
Resource Type
eISSN
21650497
Scopus ID
2-s2.0-105029481749
Pubmed ID
41416796
Journal Title
Microbiology Spectrum
Volume
14
Issue
2
Rights Holder(s)
SCOPUS
Bibliographic Citation
Microbiology Spectrum Vol.14 No.2 (2026) , e0229825
Suggested Citation
Athipanyasilp N., Saowpak S., Chaimayo C., Angkasekwinai N., Pattama A., Athipanyasilp A., Patchsung M., Aphicho K., Uttamapinant C., Horthongkham N. CRISPR-Cas13a SHERLOCK assay for rapid and sensitive detection of chikungunya virus. Microbiology Spectrum Vol.14 No.2 (2026) , e0229825. doi:10.1128/spectrum.02298-25 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/115003
Title
CRISPR-Cas13a SHERLOCK assay for rapid and sensitive detection of chikungunya virus
Author's Affiliation
Corresponding Author(s)
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Abstract
Chikungunya virus (CHIKV), a major cause of acute febrile illness and joint pain, remains a significant public health threat in tropical regions. Rapid and accurate detection is essential for timely clinical management and outbreak control, particularly in resource-limited settings where real-time PCR (RT-qPCR) is often impractical. We developed and validated a SHERLOCK assay coupled with recombinase polymerase amplification for CHIKV RNA detection. Analytical performance was assessed by determining the limit of detection (LOD), cross-reactivity, clinical sensitivity and specificity, and predictive values. The assay achieved an LOD of 215 copies/reaction with no cross-reactivity against other alphaviruses or flaviviruses. Clinical testing of 146 plasma samples showed a sensitivity and specificity of 94.52% and 100% with lateral-flow readout and 97.26% and 100% with fluorescence readout, respectively. This study establishes a promising CRISPR-Cas13a-based SHERLOCK platform for CHIKV detection, demonstrating high analytical performance, rapid turnaround time, and potential for future adaptation to resource-limited settings.IMPORTANCEEarly and accurate detection of chikungunya virus (CHIKV) is critical for outbreak control, especially in resource-limited settings, where real-time PCR is not feasible. This study demonstrates that the CRISPR-Cas13a-based SHERLOCK platform, combined with RPA, achieves high diagnostic accuracy and a low detection limit, comparable to RT-qPCR. The assay's rapid turnaround time and simple lateral-flow readout make it a promising tool for point-of-care diagnostics during CHIKV outbreaks, potentially improving disease surveillance and clinical decision-making.