RAPID: COVID-19 Detection Through Amplification of Protease-Based Signals

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The severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the cause of the novel coronavirus infectious disease 2019, COVID-19. During a key step in the viral lifecycle, infected human cells release not only virus particles but also enzymes that cut viral and host proteins, called proteases. Detection of the proteases linked to SARS-CoV-2 would provide an alternative path for testing for COVID-19. With this award, the Chemical Measurement and Imaging Program in the Division of Chemistry is supporting the research of Drs. Sankaran Thayumanavan, Jeanne Hardy, and Trisha L. Andrew at the University of Massachusetts, Amherst to develop "smart" sampling swabs whose color changes when the main protease of SARS-CoV-2 is present. The color change of the swab results when the main protease of SARS-CoV-2 breaks down a colorless, protein-derived molecule into individual pieces, with one of those pieces having its chemical properties changed during the break-down process, so that it absorbs or produces light that can be seen by the human eye. The investigators design and make the protein-derived probe molecules and then incorporate them into the fibers of currently-used clinical swabs. Their chemical design allows the probe molecules to be selectively broken down by the main protease of SARS-CoV-2 and to produce strong color in the smart swabs even when extremely low concentrations of the main protease are present. Creation of the necessary chemical reactions and their application to develop the protease-responsive smart swabs may lead to inexpensive testing methods that are practical for use by individuals at home. Due to the generality of the release of proteases in the lifecycle of viral infections, the new chemical reactions and resulting technologies are anticipated to be useful for visual detection of other viruses, which may be especially meaningful during future potential outbreaks. Educational, training, and outreach activities focus on graduate students working with Drs. Thayumanavan, Hardy, and Andrew in a cross-cutting, team-oriented research environment to address the development of front-line measurement science approaches, with anticipated highlights shared with the public and K-12 students about their experiences and lessons learned about how research funding can be used to directly impact a major societal crisis.The goal of this project is to develop rapid, accurate, straightforward probe-based sensors that detect the inherent catalytic properties of viral protease enzymes, which produce a clear optical readout. Efforts are focused on creating new sensing chemistries that utilize specifically designed dye-based reporters and using them to develop inexpensive, disposable smart swabs to detect the presence of catalytically-active severe acute respiratory syndrome coronavirus 2 main protease (CoV2-MP). The general research approach Drs. Thayumanavan, Hardy, and Andrew take is to first generate protease recognition elements by designing, producing, and validating peptides that provide the optimal specificity to the targeted viral protease. The resulting protease recognition elements are then linked to donor-acceptor chromophores to create "pro-chromophoric" probes that remain in a dark (uncolored, discolored, or quenched) state. Upon exposure to the main viral protease, the free reporter is liberated and produces a highly intense colorimetric or fluorescence signal, with the estimated limits of detection offering sensing of sub-picomolar concentrations of CoV2-MP. Sophisticated reporter formulations with integrated chemical amplification routes are predicted to provide access to these limits of detection. Importantly, the protease-based detection strategy and swab test platform are easily and generally transferable for detecting potential future viral pathogens based on their specific protease structures.This grant is being awarded using funds made available by the Coronavirus Aid, Relief, and Economic Security (CARES) Act supplemental funds allocated to MPS.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.