Abstract

Breaking the Mold: Unconventional and Powerful Point of Care Viral Diagnostics For the Post-COVID Era

Brian Cunningham, Donald Biggar Willett Professor in Engineering, University of Illinois at Urbana-Champaign

The COVID-19 pandemic offered an unprecedented urgent challenge to society’s systems for surveillance and control of a highly contagious and deadly pathogen.  However, despite their limitations, the most heavily utilized diagnostic technologies remain those based upon laboratory PCR for detection of viral nucleic acids, and lateral flow strips for self-testing of viral antigens.   Nonetheless, unconventional approaches that offer more rapid results, lower detection limits, lower cost/assay, and simpler workflows are emerging that are poised to change the existing paradigms for infectious disease detection.  As we consider preparation for potential future pandemics, we also aim to provide more effective approaches for the still-unmet needs of insect-borne viruses, HIV, animal diseases, and others.  This presentation will describe viral diagnostics using newly-developed biosensor technology combined with novel biochemistry methods demonstrated by the University of Illinois at Urbana-Champaign Center for Genomic Diagnostics since March 2020.  Beginning with microfluidic isothermal nucleic acid amplification reactions detectable with a smartphone camera for SARS-CoV-2 in saliva, we are developing a self-contained, 4x multiplexed microfluidic cartridge for detection of Zika, Dengue, and Chikungunya from a droplet of whole blood in ~20 minutes with a smartphone clip-on reader.  As an alternative to nucleic acid sequence detection, sample preparation can be greatly simplified through direct detection of intact virions.  Therefore, we developed a simple 1-step, 5-minute assay for detection of intact SARS-CoV-2 using designer DNA origami “nets” that  release fluorophores when they specifically bind with the pattern of outer spike proteins on the virus for detection with a ~$50 pocket-size smartphone-linked fluorimeter.  In a further novel approach, spike-binding DNA aptamers are used to capture intact HIV and SARS-CoV-2 virions to a photonic crystal biosensor, where they can be rapidly imaged and digitally counted through interferometric scattering of laser illumination.  Finally, we developed 1-step, room temperature, enzyme-free, ultraselective, 10-minute detection of specific RNA sequences using nucleic acid strand displacement reactions that, when combined with photonic crystal biosensor microscopy, provides ~500x lower detection limit than PCR.  The limitations of the prevailing test methods deployed to counteract SARS-CoV-2, now clearly understood, provide a roadmap for transforming pathogen detection. When fully developed, the unconventional methods will enable society to more effectively manage infectious disease.