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，由严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 引起的 2019 冠状病毒病 (COVID-19) 在全球范围内大流行。截至 2020 年 4 月 2 日，COVID-19 确诊病例已超过 100 万例，死亡人数超过 55,000 人。这些数字正在迅速增加。然而，本次疫情爆发以来的时间很短，限制了我们对 SARS-CoV-2 传播方式的了解。该项目的目标是弥补这一差距。有证据表明医疗保健提供者的感染率高得惊人，该项目将揭露医院环境中的传播模式。通过与克利夫兰诊所合作，研究人员将获得基因组、流行病学和临床患者数据。对这些数据的联合计算分析将产生一个计算模型，该模型将提供对医院传播模式的深入了解，例如从患者到医生和卫生工作者，或从医生到医生。该项目的活动将围绕三个目标进行组织。目标 1：对克利夫兰诊所收集的 SARS-CoV-2 样本进行全基因组测序。这些数据将通过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进行扩充。目标 2：建立分析管道并对目标 1 中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已识别的基因组菌株与临床数据直接联系起来。这些活动对于更好地保护医护人员和最大限度地降低医院环境中的总体感染率具有直接的临床意义。该项目的研究结果将与广大研究界分享，以帮助其他医院进行进一步分析，因为在这一流行病期间可获得更多数据。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力优势和评估进行评估，被认为值得支持。更广泛的影响审查标准。

项目成果

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

最初大流行浪潮期间急性 SARS-CoV-2 感染的宿主内突变率

• DOI: 10.1007/s11262-023-02011-0
• 发表时间: 2023-06-13
• 期刊: Virus Genes
• 影响因子: 1.6
• 作者: Kim El;T. M. Adhikari;Zheng Jin Tu;Yu;Xiaoyi Leng;Xiangyi Zhang;D. Rhoads;J. Ko;S. Worley;Jing Li;B. Rubin;Frank P Esper
• 通讯作者: Frank P Esper

Alpha to Omicron: Disease Severity and Clinical Outcomes of Major SARS-CoV-2 Variants

Alpha 到 Omicron：主要 SARS-CoV-2 变种的疾病严重程度和临床结果

• DOI: 10.1093/infdis/jiac411
• 发表时间: 2022-10
• 期刊: The Journal of Infectious Diseases
• 作者: Esper, Frank P.;Adhikari, Thamali M.;Tu, Zheng Jin;Cheng, Yu;El;Farkas, Daniel H.;Bosler, David;Rhoads, Daniel;Procop, Gary W.;Ko, Jennifer S.;et al
• 通讯作者: et al

Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity

最初的大流行浪潮期间 SARS-CoV-2 感染的基因组流行病学及其与疾病严重程度的关系

• DOI: 10.1001/jamanetworkopen.2021.7746
• 发表时间: 2021-04
• 期刊: JAMA Network Open
• 影响因子: 13.8
• 作者: Esper, Frank P.;Cheng, Yu;Adhikari, Thamali M.;Tu, Zheng Jin;Li, Derek;Li, Erik A.;Farkas, Daniel H.;Procop, Gary W.;Ko, Jennifer S.;Chan, Timothy A.;et al
• 通讯作者: et al