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

• 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
• 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

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.

该应用程序旨在开发改进的方法来检测可以大规模部署并在多种病原体中灵活的新型病原体。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。与标准的临床测试相反，在单个管中对一个人的样品进行了测试，质量测试标记每个人的样品的独特DNA，用作分子条形码，然后将多个样品汇集在一起​​，以便可以共同测试它们。然后，使用DNA测序来检测成千上万个个体的病毒样品，并根据分子条形码将病毒分配给其来自其来自的样品。台式序列器每天可以处理数万。一台较大的机器产生足够的序列，有一天可以进行数十万个测试。我们的目的是使一个中适中的分子生物学实验室能够在没有太多投资的情况下处理数万个样本。我们已经在高复杂性，CLIA认证的UCLA Swabseq Covid19测试实验室中成功部署了Swabseq测试。我们的工作证明了对高通量无症状测试的实用性，并且随着进一步的改进，可以通过数量级来提高测试能力，从而可以在人群规模上部署测试。我们的基于测序的方法可以扩展，还可以同时检测病毒变异和其他病毒病原体。群众测试将无症状载体，因此会告知公共卫生政策，以免感染的控制 有效。