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

正在进行的新冠肺炎(SARS-CoV-2)大流行凸显了我们目前诊断测试平台的局限性，以及无法在有效接触者追踪所需的人群水平上有效监测病毒传播。在采用不同检测战略的国家中，感染者的年龄人口结构的急剧变化就是例证，这导致对主要无症状但仍有传染性的人的感染流行率认识不足。通过使用自动化液体处理系统提高检测能力，将提高检测之间的一致性，节省限制试剂，并使我们能够收集更多关于病毒的信息，包括识别高危地区和人群。目前对病毒感染的检测策略主要包括逆转录定量聚合酶链式反应(RT-qPCR)，辅以全基因组鸟枪法测序，提供对病毒进化轨迹的洞察。这两种方法都需要单独处理样品，大大限制了测试吞吐量。在这份合作方案中，我们将与干细胞技术公司合作，开发和优化基于磁珠的分离技术在高通量纯化SARS-CoV-2病毒RNA方面的应用。该项目的成果包括基于96孔板和384孔板的模拟咽拭子样本的RNA自动提取，以及用于定量PCR和下一代测序(NGS)应用的扩增cDNA。干细胞积极参与与SARS-CoV-2的研究和最终治疗相关的各种研究和开发项目。与该项目相关的基础科学工作将补充更多以治疗为导向的研究项目，并帮助干细胞、学术研究人员和加拿大医疗保健部门更好地应对SARS-CoV-2大流行，提供人口水平测试和可靠的流行病学决策结果所必需的可伸缩核酸纯化方法的可操作数据。

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.