Rapid high-throughput sample preparation for COVID-19 diagnostics using integrated automation systems

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The ongoing COVID-19 (SARS-CoV-2) pandemic has highlighted limitations in our current diagnostic testing platforms and inability to effectively monitor virus spread at the population level needed for effective contact tracing. This is exemplified by drastic shifts in age demographics of infected people in countries with different testing strategies and results in insuncient understanding of the prevalence of infection in predominantly asymptomatic, but still contagious people. Increasing testing capacity through use of automated liquid handling systems will improve consistency between tests, conserve limiting reagents and allow us to collect more information about the virus including identification of high-risk areas and populations. Current testing strategies for viral infection primarily involve reverse transcription quantitative PCR (RT-qPCR), with adjunct wholegenome shotgun sequencing, providing insight into evolutionary trajectories of the virus. Both methods require individual sample processing, significantly limiting testing throughput. In this collaborarice proposal we will work with STEMCELL Technologies Inc. to develop and optimize the application of magnetic bead-based separation technology for SARS-CoV-2 viral RNA purification in high-throughput. Deliverables arising from this project include 96- and 384-well plate based automated extraction of RNA from simulated throat swab samples, as well as amplified cDNA for quantitative PCR and next generation sequencing (NGS) applications. STEMCELL is actively involved in various research and development projects related to the study and ultimate treatment of SARS-CoV-2. The basic science efforts associated with this project will complement more therapeutic oriented research projects and assist STEMCELL, academic researchers and the Canadian healthcare sector to better respond to the SARS-CoV-2 pandemic by providing actionable data on scalable nucleic acid purification methods integral to population-level testing and reliable epidemiological decision-making outcomes.