RAPID: Rapid Assay for RNA Extraction and Concentration for COVID-19 Molecular Diagnostics

Access to coronavirus testing is integral to the effort to curb and control the spread of the 2019 coronavirus disease (COVID-19). COVID-19 diagnostic tests currently implement a technique called reverse transcription-polymerase chain reaction (RT-PCR). This technique requires two reagent kits. The first is used to extract the genetic material, ribonucleic acid (RNA), from the coronavirus, and the second is used to amplify the RNA to enable its detection with RT-PCR. The current diagnostic crisis is due, in part, to shortages of the RNA extraction kits and the time required to extract the RNA using the kits. Increasing both the availability and time-efficiency of these kits is vital to improve testing accessibility and enhance the reliability of clinical diagnostics. In this project, a novel process for producing porous sorbent materials will be used to develop an alternative extraction kit for efficient and rapid extraction of nucleic acids from patient samples. The performance will be further optimized by studying the molecular mechanisms governing nucleic acid capture and release by the sorbents and applying this fundamental knowledge. The development and clinical validation of a novel extraction kit will be followed by mass production, addressing the current shortage and improving access to COVID-19 testing. The close collaboration between engineers developing the diagnostic technologies and clinicians implementing the prototypes, as enabled by this project, will streamline the transition of scientific knowledge into solutions that benefit the health and well-being of society. The project will also provide workforce development opportunities through training researchers in novel diagnostic techniques for coronaviruses.

The goal of this project is to develop a novel, scalable approach to nucleic acid separation and concentration and mass-produce prototype kits for immediate implementation in clinical settings. The concept relies on the use of sorbent materials instead of the current filter- and silica column-based approach. Unlike filters that use pore size to physically separate the target (here nucleic acids) from the media, sorbents are a porous material that captures the target by chemical affinity and interactions. As a result, the use of a sorbent enables larger water flow rates, enhanced nucleic acid capture efficiency, and faster sample processing, and overcomes the need for multiple buffers or extraction steps. Functionalization of conventional filters with a combination of metal oxide nanoparticles and organosiloxane polymers will be used to produce the nucleic acid sorbent. The functionalization will be achieved by a new method for supported synthesis of nanoparticles by thermolysis and polymer conjugation. The efficiency of the sorbent will be assessed by the extraction and detection of nucleic acid using quantitative RT-PCR. Validation of the alternative sorbent kit will assess the effectiveness of the rapid separation and concentration of the novel coronavirus (SARS-CoV-2) RNA. The project will also explore the fundamentals of nucleic acid dynamics in porous sorbents as it relates to nucleic acid size, sorbent chemistry, porosity and pore size, and the effect of transport phenomena in porous media. Enhanced understanding of the factors that affect the retention, release, and transport of nucleic acids in porous media is critical to producing reliable and efficient nucleic acid extraction and detection kits and the development of other bio-separation processes. Training of postdoctoral researchers and graduate and undergraduate students will focus on how the combination of transdisciplinary collaboration and a clear understanding of the fundamental aspects can lead to disruptive technologies.

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.