SARS-CoV2 sequencing surveillance program for Upstate South Carolina

南卡罗来纳州北部 SARS-CoV2 测序监测计划

• 批准号: 10381278
• 负责人: Hai Yao
• 金额: $ 12.5万
• 依托单位: CLEMSON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381278
• 关键词: 2019-nCoV; Area; Bioinformatics; CLIA certified; COVID testing; COVID-19; COVID-19 testing; COVID-19 vaccination; COVID-19 vaccine; Cities; Clinical; Communities; Country; Data; Data Collection; Databases; Diagnosis; Diagnostic; Disadvantaged; Disease; Disease Outbreaks; Education; Ensure; Event; Genomics; Geographic Locations; Goals; Health; Health care facility; Hospitals; Human Resources; Individual; Infection; Instruction; Intervention; Measures; Monitor; Nature; Outcome; Patients; Persons; Policies; Population; Population Surveillance; Positioning Attribute; Prevalence; Process; Public Health; Research; Research Personnel; Reverse Transcriptase Polymerase Chain Reaction; Risk; Running; Rural; SARS-CoV-2 B.1.1.7; SARS-CoV-2 genome; SARS-CoV-2 infection; SARS-CoV-2 positive; Saliva; Sampling; Severities; Severity of illness; Site; South Carolina; Students; Surveillance Program; Symptoms; System; Testing; Time; Travel; Universities; Vaccination; Variant; Viral Load result; Virulent; Virus; Work; data mining; demographics; disease diagnosis; experience; falls; genetic variant; genome sequencing; illness length; insight; member; outreach; pandemic disease; patient population; programs; undergraduate student; variants of concern

Project Summary The goal of this project is to leverage the extensive COVID-19 testing program at Clemson University (CU) to detect and monitor emerging variants of the SARS-CoV2 virus by sequencing every positive sample. Variants of concern are emerging in our state of South Carolina. This is a serious public health threat because there is a real risk that these new variants may escape the coverage of recently developed COVID-19 vaccines or infect previously exposed individuals. This sequencing project will provide much-needed insight and guidance to inform policy decisions in our region and elsewhere to help mitigate these potential threats. In Fall 2020, CU established the new CLIA-certified Clemson Research and Education in Disease Diagnosis and Intervention (REDDI) Lab. In what has become one of the robust COVID-19 testing programs in the country, the REDDI Lab tests of all university personnel and students at least once a week with their own highly accurate saliva COVID-19 RT-PCR test, developed and validated by researchers at Clemson shortly after the start of the pandemic. The lab also provides free testing to members of the surrounding upstate SC community. It processes 99.9% of its tests within 24hrs and currently averages over 20,000 tests per week, a substantial fraction of all testing in the state. We propose the following aims: Aim 1: Implement a SARS-CoV2 genomic sequencing workflow and a data collection system to use a large established COVID-19 testing program in rural, upstate South Carolina. Aim 2: Determine the association of SARS-CoV2 genomic variants with population demographics, outbreak events, COVID-19 symptom severity and duration, previous infection, and vaccination. Given the capabilities of the REDDI Lab and the state-of-the-art Clemson University Genomics and Bioinformatics Facility (CUGBF), we are ideally positioned to build a robust and informative sequencing and surveillance program. Due to proximity to major travel hubs (Charlotte / Atlanta) and the transient nature of a university population, many variants will likely appear in our testing pool. More importantly, we will capture data from patient demographic groups that are highly under-sampled by other labs at hospitals and public health agencies. Unlike many of these COVID testing programs, the majority of positive cases detected by our lab are from younger patients (students) who are asymptomatic or minimally symptomatic at the time of diagnosis. In addition, the Clemson public health initiatives partnering with our testing lab include free daily testing for the community using a standing site in the city of Clemson and a mobile testing van that provides outreach to disadvantaged areas of the Upstate where COVID-19 testing is not easily available. Our community testing population is an excellent representation of the Upstate SC demographics, including significant numbers of patients from populations with known COVID-19 outcome disparities.

项目摘要 该项目的目标是利用克莱姆森大学（CU）广泛的COVID-19检测项目， 通过对每个阳性样本进行测序，检测和监测新出现的SARS-CoV 2病毒变异。的变体 在我们南卡罗来纳州出现了一种担忧这是一个严重的公共卫生威胁，因为有一个 真实的风险是，这些新的变异可能会逃脱最近开发的COVID-19疫苗的覆盖范围，或感染 以前接触过的人。这个测序项目将提供急需的洞察力和指导， 为我们区域和其他地方的政策决定提供信息，以帮助减轻这些潜在的威胁。 2020年秋季，CU建立了新的CLIA认证的克莱姆森疾病诊断研究和教育中心 干预（REDDI）实验室在已经成为该国强有力的COVID-19检测项目之一的项目中， REDDI实验室每周至少对所有大学人员和学生进行一次测试， 唾液COVID-19 RT-PCR测试，由克莱姆森的研究人员在开始后不久开发和验证， 流行病该实验室还提供免费测试，以周围的北部SC社区的成员。It流程 99.9%的测试在24小时内完成，目前平均每周超过20，000次测试，占所有测试的很大一部分。 测试在国家。 我们提出以下目标： 目标1：实施SARS-CoV 2基因组测序工作流程和数据收集系统，以使用大型 在南卡罗来纳州北部的农村地区建立了COVID-19检测项目。 目的2：确定SARS-CoV 2基因组变异与人口统计学、疫情暴发 事件、COVID-19症状严重程度和持续时间、既往感染和疫苗接种。 鉴于REDDI实验室和最先进的克莱姆森大学基因组学的能力， 生物信息学设施（CUGBF），我们是理想的定位，以建立一个强大的和信息丰富的测序和 监视程序。由于靠近主要的旅游枢纽（夏洛特/亚特兰大）和短暂的性质， 在大学人群中，许多变体可能会出现在我们的测试池中。更重要的是，我们将收集数据， 来自医院和公共卫生部门其他实验室高度低采样的患者人口统计组 社.与许多这些COVID检测项目不同，我们实验室检测到的大多数阳性病例是 来自诊断时无症状或症状轻微的年轻患者（学生）。在 此外，与我们的测试实验室合作的克莱姆森公共卫生倡议包括免费的每日测试， 社区使用克莱姆森市的一个常设站点和一辆移动的测试货车， 上州的贫困地区，那里不易获得COVID-19检测。我们的社区测试 人口是上州SC人口统计的一个很好的代表，包括大量的 来自已知COVID-19结局差异人群的患者。