Expanding Swabseq sequencing technology to enable readiness for emerging pathogens

扩展 Swabseq 测序技术，为新出现的病原体做好准备

基本信息

批准号：
10719421
负责人：
Valerie A Arboleda
金额：
$ 57.35万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-11 至 2028-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10719421
关键词：
2019-nCoV Algorithmic Analysis Area Bar Codes Biological Assay CLIA certified COVID-19 COVID-19 detection COVID-19 pandemic COVID-19 screening COVID-19 testing Calibration Cessation of life Clustered Regularly Interspaced Short Palindromic Repeats Coccidioidomycosis Collection Communicable Diseases Contact Tracing Containment Coupled DNA DNA sequencing Detection Diagnosis Disease Disease Outbreaks Excision Failure Genomics Goals Health Health Policy Hospitalization Hour Human Human poliovirus Individual Infection International Investments Label Laboratories Light Link Masks Mass Screening Measures Methodology Methods Molecular Molecular Biology Monkeypox Nested PCR Nucleic Acids Patients Persons Poliomyelitis Population Probability Process Protocols documentation Public Health Quarantine RNA Rapid screening Reaction Readiness Reagent Research Reverse Transcriptase Polymerase Chain Reaction Reverse Transcription Running Sampling Series Specimen Swab Symptoms Technology Test Result Testing Time Travel Tube Vaccination Variant Viral Virus Vision Work clinical development clinical diagnostics combinatorial commensal bacteria cost current pandemic desert fever design detection limit detection method emerging pathogen flexibility future pandemic high throughput screening improved indexing innovation next generation next generation sequencing novel pandemic disease pandemic response pathogen pathogenic bacteria pathogenic fungus pathogenic virus research clinical testing saliva sample scale up surveillance network technology development transcriptome sequencing transmission process variant detection viral detection

项目摘要

This application aims to develop improved methods for detecting novel pathogens that can be deployed on a large scale and are flexible to multiple pathogens. The method uses the power of next generation sequencing technology to analyse hundreds of thousands of samples simultaneously. In contrast to standard clinical testing, where one person's sample is tested in a single tube, mass testing labels each person's sample with a unique piece of DNA that acts as a molecular barcode, then pools multiple samples together so that they can be jointly tested. DNA sequencing is then used to detect those samples with virus in the pool of hundreds of thousands of individuals, and assign the virus to the samples it came from on the basis of the molecular barcodes. A bench top sequencer can process tens of thousands a day. A larger machine generates enough sequence to run up to hundreds of thousands of tests in one day. Our aim is to make it possible for a moderately well-equipped molecular biology laboratory to be able to process tens of thousands of samples without much investment. We have successfully deployed SwabSeq testing at the high-complexity, CLIA-certified, UCLA SwabSeq COVID19 Testing laboratory. Our work has demonstrated the utility for high-throughput asymptomatic testing and with additional improvements can increase testing capacity by orders of magnitude, making it possible to deploy testing on a population scale. Our sequencing-based approach can be extended to also detect viral variants at the same time and to other viral pathogens. Mass testing will f nd asymptomatic carriers and thus inform public health policies so that containment of infection will be effective.

该应用旨在开发改进的方法来检测新型病原体，这些方法可以大规模部署并且灵活地检测多种病原体。该方法利用下一代测序技术的力量同时分析数十万个样本。与标准临床测试（其中一个人的样本在单管中进行测试）不同，大规模测试用一段独特的 DNA（充当分子条形码）标记每个人的样本，然后将多个样本汇集在一起，以便可以对它们进行联合测试。然后使用 DNA 测序来检测数十万个体中带有病毒的样本，并根据分子条形码将病毒分配给其来源的样本。台式测序仪每天可以处理数以万计的数据。一台更大的机器生成足够的序列，可以在一天内运行多达数十万个测试。我们的目标是让一个设备中等的分子生物学实验室能够在不需要太多投资的情况下处理数万个样本。我们已在高复杂性、CLIA 认证的加州大学洛杉矶分校 SwabSeq COVID19 检测实验室成功部署了 SwabSeq 检测。我们的工作证明了高通量无症状检测的实用性，并且通过额外的改进可以将检测能力提高几个数量级，从而可以在人口规模上部署检测。我们基于测序的方法可以扩展到同时检测病毒变异体和其他病毒病原体。大规模检测将发现无症状携带者，从而为公共卫生政策提供信息，从而遏制感染要有效果。