RAPID:Genomic Variation Analysis of Coronavirus to Better Understand the Spread of COVID-19

RAPID：冠状病毒的基因组变异分析，以更好地了解 COVID-19 的传播

• 批准号: 2027667
• 负责人: Jing Li
• 金额: $ 12.44万
• 依托单位: Case Western Reserve University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2027667&HistoricalAwards=false
• 关键词: RAPID; Genomic; Variation; Analysis; Coronavirus

Currently, there is a world-wide pandemic of the Coronavirus Disease 2019 (COVID-19) that is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of April 2, 2020, there have been more than one million confirmed cases of COVID-19 and more than 55,000 deaths. These numbers are increasing rapidly. Yet, the short time since the beginning of this outbreak limits our understanding of how SARS-CoV-2 spreads. The objective of this project is to address this gap. In response to evidence that the rate of infections among healthcare providers is alarmingly high, this project will expose transmission patterns in the hospital setting. In collaboration with the Cleveland Clinic, the investigators will have access to genomic, epidemiological, and clinical patient data. Joint computational analysis of this data will result in a computational model that will provide insights into transmission patterns in hospitals, such as from patients to doctors and health workers, or from doctors to doctors. The activities in this project will be organized along three Aims. Aim 1: Perform whole-genome sequencing of SARS-CoV-2 samples collected at the Cleveland Clinic. The data will be augmented by existing SARS-CoV-2 sequence data from multiple online databases, as well as existing sequence data from other species. Aim 2: Build an analysis pipeline and perform evolutionary analysis of genomic data obtained in Aim 1. Aim 3: Perform joint analysis of genomic, epidemiological, and clinical data to infer transmission patterns. One of the unique advantages of the project is the ability to directly link identified genomic strains to clinical data. The activities have direct clinical implications for better protecting healthcare workers and minimizing the overall rate of infections in the hospital setting. Findings from this project will be shared with the research community at large to aid further analysis in other hospitals as more data becomes available during this pandemic.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.

目前，2019年冠状病毒病（COVID-19）的全球大流行是由严重的急性呼吸综合征冠状病毒2（SARS-COV-2）引起的。截至2020年4月2日，已有超过一百万个证实的1900案病例和55,000多人死亡。这些数字正在迅速增加。但是，自爆发开始以来的短时间内，我们对SARS-COV-2如何传播的理解限制了我们的理解。该项目的目的是解决这一差距。为了回应证据表明，医疗保健提供者之间的感染率令人震惊，该项目将在医院环境中暴露传播模式。与克利夫兰诊所合作，研究人员将可以访问基因组，流行病学和临床患者数据。该数据的联合计算分析将导致一个计算模型，该模型将为医院的传播模式提供见解，例如从患者到医生和卫生工作者，或者从医生到医生。该项目中的活动将以三个目标进行。目标1：对克利夫兰诊所收集的SARS-COV-2样品进行全基因组测序。来自多个在线数据库的现有SARS-COV-2序列数据以及其他物种的现有序列数据将增加数据。目标2：建立分析管道并对目标1获得的基因组数据进行进化分析。目标3：对基因组，流行病学和临床数据进行联合分析以推断传播模式。该项目的独特优势之一是能够将确定的基因组菌株与临床数据直接联系起来。这些活动具有直接的临床意义，可以更好地保护医疗人员，并最大程度地减少医院环境中感染的总体感染率。该项目的调查结果将与整个研究界分享，以帮助其他医院进行进一步的分析，因为在此大流行期间获得了更多数据。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子和更广泛影响的评估审查标准来通过评估来支持的。

项目成果

Intra-host mutation rate of acute SARS-CoV-2 infection during the initial pandemic wave

• DOI: 10.1007/s11262-023-02011-0
• 发表时间: 2023-06
• 期刊: Virus Genes
• 影响因子: 1.6
• 作者: Kim El-Haddad;T. M. Adhikari;Zheng Jin Tu;Yu-Wei Cheng;Xiaoyi Leng;Xiangyi Zhang;D. Rhoads;J. Ko;S. Worley;Jing Li;B. Rubin;Frank P Esper