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: 10655672
• 负责人: Xiaohu Yao
• 金额: $ 45万
• 依托单位: ATOM BIOWORKS INC
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-06 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10655672
• 关键词: 2019-nCoV; Affect; Affinity; Antibody Response; Antigens; Architecture; Avidity; Binding; Biological Assay; Biosensing Techniques; Biosensor; Blood Coagulation Disorders; Blood coagulation; COVID-19 detection; COVID-19 diagnostic; COVID-19 monitoring; COVID-19 pandemic; Cells; Cessation of life; Chronic Disease; Complex; DNA; Dengue Virus; Detection; Development; Diabetes Mellitus; Diagnostic; Disease; Epitopes; Heart failure; Hospitals; Hypertension; Immunoassay; Impairment; Individual; Infection; Infectious Agent; Infrastructure; Laboratories; Lead; Link; Location; Modality; Molecular; Monitor; Nanostructures; Patients; Pattern; Persons; Plasma; Preparation; Quarantine; Rapid diagnostics; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 infection; Saliva; Sampling; Schools; Sensitivity and Specificity; Specificity; Surface; Surface Antigens; Symptoms; System; Testing; Time; Urine; Viral; Virion; Virus; Whole Blood; antibody detection; aptamer; base; cost; cost effective; detection assay; heart function; instrument; novel; pandemic disease; particle; pathogen; pathogenic virus; pulmonary function; rapid testing; rational design; response; saliva sample; sample collection; viral detection

ABSTRACT A Novel Saliva-Based Aptamer Detection Assay for SARS-CoV-2 Infection 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 一种新的唾液适体检测SARS-CoV-2感染方法 需要自动、快速的诊断，只需很少的样本收集和准备即可确定 并在高传染性病原体导致大流行的时候追踪受影响的人。频繁， 低成本和高度可扩展的测试是了解 并最终控制疾病的传播。我们建议开发一种 独特的系统，可以廉价和容易地检测唾液样本中的SARS-CoV-2。这个 开发一种使用唾液的系统提供了一个机会，可以方便地使用 易于采集且含有高浓度病毒颗粒的样本。 SARS-CoV-2大流行主要影响有既往疾病的个人 如凝血障碍、糖尿病、高血压或其他慢性病。患有这些疾病的患者 先前存在的疾病，然后被感染，会加剧症状和并发症， 可能会导致死亡。例如，许多死于SARS-CoV-2感染的患者 出现血栓，损害肺或心脏功能，并最终 心力衰竭。使用容易收集的样本(例如唾液)进行快速诊断将允许 感染被更快地发现，治疗被更快地实施，治疗被监测， 最终导致较少的人死于这种感染。 我们概述了一种新的DNA Star生物传感方法，该方法基于这样一个事实，即病毒，如SARS- CoV-2，在其表面表达独特的抗原空间模式，促进多价 与宿主细胞结合以进行感染。这些表位的配置推动了高灵敏度和 我们化验的特异性。基于这种自然产生的结合机制，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器DNA架构。 开发了一种概念验证登革病毒(DENV)快速诊断方法，以演示其 力量：DENV表面抗原呈现出所有已知的最复杂的几何图案 病原体，一种DNA星形连接的10适配子纳米结构，提供多价、空间DENV- 表位模式匹配相互作用提供了高的DENV结合亲和力和特异性， 与传统的适体方法相比，亲和力提高了约1,000倍 单价适配子-表位相互作用。我们的POCT诊断检测到完整的DENV病毒粒子 患者样本在&lt；2分钟内具有等同的PCR敏感性，费用为&lt；$0.15。 目前的RT-PCR分子检测适用于大型、集中化、难以规模化的实验室 用于快速检测样本并将结果提供给临床医生和患者。免疫分析测试 敏感性较低，患者需要对病毒产生反应才能检测到 抗体反应。我们的“DNA STAR”基于生物传感器的快速诊断将提供 用于SARS-CoV-2实时诊断的基础设施，易于使用(无需仪器)，速度更快 (样本到结果在几分钟内)和成本效益(每项测试约3美元)。