Designer DNA Nanostructure Based Biosensing for Rapid COVID19 Detection and Monitoring using Saliva Sample

基于 DNA 纳米结构的设计生物传感，使用唾液样本快速检测和监测新冠肺炎

• 批准号: 10266426
• 负责人: Xiaohu Yao
• 金额: $ 125.8万
• 依托单位: ATOM BIOWORKS INC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-21 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10266426
• 关键词: 2019-nCoV; Affect; Affinity; Americas; Antibody Response; Antigens; Architecture; Avidity; Binding; Biochemistry; Biological Assay; Biological Markers; Biosensing Techniques; Biosensor; Blood Coagulation Disorders; Blood Volume; Blood coagulation; COVID-19 assay; COVID-19 detection; COVID-19 diagnostic; COVID-19 monitoring; COVID-19 pandemic; Cells; Cessation of life; Chronic Disease; Clinical; Communicable Diseases; Complex; Computer software; Contact Tracing; DNA; Data Analytics; Dengue Virus; Detection; Development; Devices; Diabetes Mellitus; Diagnostic; Diagnostic tests; Disease; Education; Epitopes; Future; Hand; Heart failure; Hospitals; Hypertension; Illinois; Immunoassay; Impairment; Individual; Infection; Infectious Agent; Infrastructure; Laboratories; Lead; Link; Location; Louisiana; Medical Device; Modality; Molecular; Monitor; Nanostructures; Patients; Pattern; Persons; Physicians; Pilot Projects; Plasma; Preparation; Quarantine; Rapid diagnostics; Reagent; Recommendation; Research; Reverse Transcriptase Polymerase Chain Reaction; Risk; Running; SARS-CoV-2 infection; Saliva; Sampling; Schools; Sensitivity and Specificity; Site; Small Business Technology Transfer Research; Societies; Specificity; Surface; Surface Antigens; Symptoms; System; Testing; Time; Universities; Urine; Validation; Viral; Viral Load result; Virion; Virus; Whole Blood; antibody detection; aptamer; base; biomarker panel; cost; cost effective; design; detection assay; detection platform; diagnostic assay; diagnostic platform; experience; heart function; improved; innovation; instrument; multidisciplinary; novel; novel strategies; pandemic disease; particle; pathogen; pathogenic virus; prototype; pulmonary function; rapid testing; response; saliva sample; salivary assay; sample collection; viral detection

ABSTRACT A Novel Saliva-Based Aptamer Detection Assay for SARS-CoV-2 Infection (RFA-OD-20-021 STTR Application) Automated, rapid diagnostics with little sample collection and preparation are needed to identify and trace affected persons in times when hyper-infectious pathogens cause pandemics. Frequent, low cost and highly scalable testing is the only way to gain visibility on the magnitude of the pandemic and ultimately control the spread of the disease. We propose the development of a unique system that can cheaply and readily detect SARS-CoV-2 in saliva samples. The development of a system that uses saliva present an opportunity to readily test patients using a sample that is easily collected and harbors high concentration of viral particles. The SARS-CoV-2 pandemic has predominantly affected individuals with pre-existing conditions such as clotting disorders, diabetes, hypertension or other chronic diseases. Patients with these pre-existing conditions who then are infected have exacerbated symptoms and complications that can lead to death. For example, many patients that have succumbed to SARS-CoV-2 infection have developed blood clots that have impaired pulmonary or cardiac function and ultimately cardiac failure. A rapid diagnostic using easily collected samples (e.g. saliva) would allow for infections to be identified sooner, therapies to be administered quicker, treatment to be monitored, and ultimately leading to fewer individuals that succumb to the infection. We outline a novel DNA Star biosensing approach based on the fact that viruses, such as SARS- CoV-2, express unique spatial patterns of antigens on their surfaces, facilitating multivalent binding to host cells for infection. These configurations of epitopes drive the high sensitivity and specificity of our assay. Based on this naturally occurring binding mechanism, we developed a rational design approach producing pattern matching designer DNA architecture for viral sensing. A proof-of-concept Dengue virus (DENV) rapid diagnostics was developed to demonstrate its power: DENV surface antigens present the most complex geometric pattern among all known pathogens, a DNA star linked 10-aptamers nanostructure that offers polyvalent, spatial DENV- epitope pattern matching interactions has provided high DENV-binding avidity and specificity, increasing affinity by ~1,000× compared to the conventional aptamer approach which relies on monovalent aptamer-epitope interactions. Our POCT diagnostics detected intact DENV virions in patient samples with PCR equivalent sensitivity in <2 mins at a cost <$0.15. Current RT-PCR molecular test are suited to large, centralized laboratories, and difficult to scale for rapid testing of samples and delivery of results to clinicians and patients. Immunoassay tests have lower sensitivity, and patients need to develop a response to the virus in order to detect the antibody response. Our “DNA star” biosensor-based rapid diagnostics will provide the infrastructure for real time SARS-CoV-2 diagnostics that is easy to use (instrument-free), faster (sample to results in minutes) and cost effective (~$3 per test).

摘要 一种新的SARS-CoV-2唾液核酸适体检测方法 （RFA-OD-20-021 STTR应用） 需要自动化、快速的诊断，只需很少的样品收集和制备， 并在高传染性病原体引起流行病时追踪受影响的人。频繁， 低成本和高度可扩展的测试是唯一的方法，以获得可见性的大小， 并最终控制疾病的蔓延。我们建议发展一个 这是一个独特的系统，可以廉价和容易地检测唾液样本中的SARS-CoV-2。的 使用唾液的系统的开发提供了一个机会， 容易收集并含有高浓度病毒颗粒的样本。 SARS-CoV-2大流行主要影响先前存在疾病的个人 例如凝血障碍、糖尿病、高血压或其它慢性疾病。这些患者 先前存在的疾病，然后被感染，加剧了症状和并发症， 可能会导致死亡。例如，许多死于SARS-CoV-2感染的患者 已经形成了损害肺或心脏功能的血栓， 心力衰竭使用容易收集的样品（例如唾液）的快速诊断将允许 更快地发现感染，更快地给予治疗，监测治疗， 并最终导致更少的人死于感染。 我们概述了一种新的DNA星星生物传感方法的基础上的事实，病毒，如SARS- CoV-2在其表面上表达独特的抗原空间模式，从而促进多价抗原的形成。 与宿主细胞结合用于感染。表位的这些构型驱动了高灵敏度， 我们检测的特异性。基于这种天然存在的结合机制，我们开发了一种 合理的设计方法，产生用于病毒传感的模式匹配设计者DNA结构。 开发了一种概念验证的登革热病毒（DENV）快速诊断方法，以证明其 功效：DENV表面抗原在所有已知的抗原中呈现最复杂的几何图案。 病原体，DNA星星连接的10-适体纳米结构，提供多价，空间DENV- 表位模式匹配相互作用提供了高DENV结合亲合力和特异性， 与传统的适配体方法相比，亲和力增加约1，000倍， 单价适体-表位相互作用。我们的POCT诊断检测到完整的DENV病毒粒子， 在<2分钟内以<0.15美元的成本获得具有PCR等效灵敏度的患者样本。 目前的RT-PCR分子检测方法适用于大型、集中的实验室，难以规模化 用于样品的快速检测以及将结果传送给临床医生和患者。免疫分析检测 敏感性较低，患者需要对病毒产生反应才能检测到病毒。 抗体反应我们的“DNA星星”生物传感器为基础的快速诊断将提供 用于真实的实时SARS-CoV-2诊断的基础设施，易于使用（无需仪器），速度更快 （样品在几分钟内得到结果）和成本效益（每个测试约3美元）。