SBIR Phase I: RAPID Integrated and automated genomics platform for hospitals responding to COVID-19

这项小企业创新研究（SBIR）第一阶段项目的更广泛影响/商业潜力将是一个用户友好且可扩展的感染控制监测软件平台，使用先进的生物技术和数据分析来监测COVID-19大流行。2019冠状病毒病大流行凸显了快速检测、分析和跟踪的必要性。这项创新为医疗机构提供了下一代测序技术，以及一个集中式系统，可以集成和共享医院级数据，并在任何地理范围内共享微生物信息。该平台可以自动分析细菌和病毒数据，通过交互式网络界面提供简化的临床相关结果。提出的技术为临床医生和其他专家提供了重要的数据。这个SBIR一期项目的智力优势在于生成最大的SARS-CoV-2全基因组和匹配的呼吸微生物组，供临床医生快速测试用于诊断和处方使用的医学假设。我们的项目有三个主要目标：1)建立一个自动化分析管道来处理SARS-CoV-2感染菌株的全基因组；2)整合病毒基因组与患者微生物组和临床记录；3)通过交互式web界面提供清晰，易于解释的结果。基于云的感染控制软件平台解决方案使病原体基因组学与临床和患者人口统计学相结合的“精确流行病学”成为可能，从而改善患者预后，增强卫生系统感染控制和监测的能力。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase I project will be a user-friendly and scalable infection control surveillance software platform using advanced biotech and data analytics for monitoring the COVID-19 pandemic. The COVID-19 pandemic highlights the need for rapid testing, analysis, and tracking. The innovation provides access to next-generation sequence technologies to healthcare facilities, as well as a centralized system to integrate and share hospital-level data with microbial information to be shared on any geographic scale. The platform automates the analysis of bacterial and viral data, delivering simplified and clinically relevant results via interactive web interfaces. The proposed technology offers important data to clinicians and other experts. The intellectual merit of this SBIR Phase I project is to generate the largest collection of SARS-CoV-2 whole genomes with matched respiratory microbiomes for clinicians to rapidly test medical hypotheses for diagnostic and prescriptive use. Our project has three major objectives: 1) incorporate an automated analytical pipeline to process whole genomes of infecting strains of SARS-CoV-2; 2) integrate viral genomes with patient microbiomes and clinical records, and; 3) deliver clear, easy-to-interpret results via an interactive web interface. The infection control cloud-based software platform solution enables “precision epidemiology” integrating pathogen genomics with clinical and patient demographics to improve patient outcomes and enhance the capability of the health system for infection control and surveillance.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.