Rapid and portable quantification of HIV RNA via a smartphone-enabled digital CRISPR device and deep learning

Abstract

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 engineer a palm-size device measuring 70 × 115 × 80 mm and weighing less than 0.6 kg. We also capitalized the smartphone by developing a custom app to control the device, perform the digital assay, and capture fluorescence images throughout the assay using the smartphone's camera. Moreover, we trained and verified a deep learning-based algorithm for analyzing fluorescence images and identifying positive digital reaction wells with high accuracy. Using our smartphone-enabled digital CRISPR device, we successfully detected as low as 75 copies of HIV RNA in just 15 min, showing its potential toward monitoring of HIV viral loads and aiding the global effort to combat the HIV/AIDS epidemic.