RAPID: High-Throughput and Low-Cost Testing of COVID-19 Viruses and Antibodies through Compressed Sensing and Group Testing

Large-scale, high-throughput and accurate COVID-19 virus and antibody testings are vital tools in the fight against the ongoing COVID-19 pandemic. Public health experts believe that mass virus and antibody testings are essential to stopping spread of COVID-19 viruses, and enabling a safe and fast transition to normal social life. However, current testing capacity is limited, and, in addition, there is often a shortage of reagents needed for performing tests. There is an urgent need to increase the current testing capacity in the United States and around the world. This Rapid Response Research (RAPID) project seeks to significantly increase the throughputs of COVID-19 virus and antibody testing, and reduce reagent consumptions through mathematical and signal processing methods, without sacrificing test accuracy. This project promotes the science of detecting and quantifying virus and antibody. This project serves the national interest and advances national health, prosperity and welfare by enabling large-scale COVID-19 virus and antibody testing, effective contact tracing and a safer, faster transition back to normal economic activities. The methods proposed in this project are also applicable to testing for other infectious diseases. If successful, research outputs from this project can be used as lively examples to inspire the public and K-12 students' interest in STEM education and research by showing the power of STEM in fighting the pandemic.

One simple method to increase the effective testing capacity is to perform testing on pooled samples of a number of subjects collectively instead of testing samples from each person individually. Pooled testing has been successfully used for infectious disease testing such as Human Immunodeficiency Virus in the past. While a simple version of this idea called group testing goes back many decades, this project proposes to develop a novel more powerful and general type of pooled testing based on the compressed sensing theory, which includes group testing as a special case. In virus testing, standard swab tests use the Reverse Transcription Polymerase Chain Reaction (PCR) process to selectively amplify DNA strands produced by viral RNA specific to COVID-19 viruses. The widely used quantitative PCR (qPCR) process allows not only binary detection (presence or absence) of a target RNA sequence, but also quantification of the RNA, producing estimates of the quantity of the RNA in test samples. This quantification can enable compressed sensing for pooled testing in virus testing, which can potentially significantly increase test throughput, reduce the number of needed tests, reduce consumption of scarce reagents, and provide quantitative results robust against observation noises and outliers. The proposed work includes designing optimized pooled measurements, and optimized inference algorithms for compressed sensing and group testing in COVID-19 virus and antibody testing.

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.