CRISPR-based diagnostics for rapid infectious disease detection development, optimization, and point of care implementation

Author(s): Reyam Moeen Abed
Date: 08/10/2026
doi: https://doi.org/10.5281/zenodo.8425890

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Abstract

The CRISPR-based diagnostics capitalizes on the collateral activity of Cas12 and Cas13 to detect nucleic 
acids specific to the diagnostic target at high speed. Detectors like DETECTR and SHERLOCK have been 
deployed during the SARS CoV-2 pandemic, and have given rise to amplification free, multiplexed, and 
paper based formats. The current study describes an experimental pipeline to design and validate a 
CRISPR Cas diagnostic of an RNA virus model based on simulated clinical samples. It compares 
isothermal amplification of a single pot of RT RPA/RT LAMP with CRISPR readout amplification to 
amplification free Cas13 detection. Optimized one pot workflows can detect limits similar to RT qPCR 
within less than 40 minutes, and amplification free Cas13 assays can detect amounts of approximately 102 
copies/µl of multiplexed crRNAs and improve signal capture to a level suitable to screening applications. 
Issues such as sample preparation, reagent stability, multiplexing, and regulatory obstacles are addressed, 
and approaches to point of care implementation discussed. The results reveal the future potential of 
CRISPR diagnostics to be used in rapid epidemic response and indicate future development of non-nucleic 
acid targets using aptamer based modules. 

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