Detection and Automatic Privacy-Protected Contact Tracing System Designed for COVID-19

Project Summary/Abstract The COVID-19 pandemic has rapidly spread across the world, bringing death, illness, disruption to dailylife, and economic crisis to businesses and individuals. The situation has been exacerbated after the schoolsand companies reopened due to economic pressure. One of the key failures in COVID-19 containment isunderlined by the inability of our healthcare system in real-time detection in point-of-care (POC) and end-usersettings and precise tracing with privacy protection of active infections. The fundamental limitations of currentgene-based assays stem from their reliance upon amplification and detection of the viral genetic materialseven if there were no intact/infectious viruses. These tests require labor-intensive, laboratory-based samplepreparation protocols for virus lysis, extraction of genetic materials, purification of the isolated materials,thermal cycling for enzymatic amplification of viral nucleic acid sequences, and interpretation of complexresults by professionals. To accurately determine the infectivity of the infected individuals, contaminatedobjects and environments, and provide guidance for patients, public and authorities to better manage treatmentand containment, we seek a new paradigm for rapid and direct pathogen detection and identification in whichthe intact virions are directly recognized through their distinct surface epitope features, and the resultantfluorescent signal is immediately captured by an end-user smartphone, followed by automatic data transitionand event tracing in a blockchain-encrypted manner. To achieve specific recognition of SARS-CoV-2 virions,we customized a designer DNA nanostructure (DDN)-based capture probe that harbors a macromolecular"net" whose vertices precisely match the intra- and inter-spatial pattern of SARS-CoV-2 trimeric spikeglycoprotein clusters, and integrates a net-shaped array of SARS-CoV-2 spike specific-targeting aptamers.This aptamer-DDN is designed for maximum affinity and specificity binding with spikes on intact virions in apolyvalent and pattern-matching fashion. Once bound to intact virions, the DNA "nets" trigger the release offluorescence. This fluorescent signal can be readily and automatically detected by a membrane-shaped andsmartphone-based fluorimeter attached to the end-users' phone cameras. The acquired results will beassociated with user device IDs that are cyber-protected before tracing. We propose to combine DDN captureprobes and a smartphone device to develop and demonstrate a rapid, room temperature, single-step, virus-specific, and ultrasensitive detection of SARS-CoV-2 virus, in which the detection results can be acquiredwithin 5 minutes upon exposure, at the user end, allowing tracing the presence of viruses without affecting userprivacy. The signal to result transition, result to ID association, individual track and interacting network tracingwill be blockchain-encrypted to ensure information security for individual privacy, while tracing informationwould be available to health authority for public health benefits.