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For the 29.8 million people in the world living with HIV/AIDS and receiving antiretroviral therapy, it is crucial to monitor their HIV viral loads. To this end, rapid and portable diagnostic tools that can quantify HIV RNA are critically needed. We report herein a rapid and quantitative digital CRISPR-assisted HIV RNA detection assay that has been implemented within a portable smartphone-based device as a potential solution. Specifically, we first developed a fluorescence-based reverse transcription recombinase polymerase amplification (RT-RPA)-CRISPR assay that can efficiently detect HIV RNA at 42°C. We then implemented this assay within a commercial stamp-sized digital chip, where RNA molecules were quantified as strongly fluorescent digital reaction wells. The isothermal reaction condition and the strong fluorescence in the digital chip simplified the design of thermal and optical modules, allowing us to …