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 该项目的目的是利用克莱姆森大学（CU）的广泛的Covid-19测试计划 通过对每个阳性样品进行测序，检测和监测SARS-COV2病毒的新兴变体。变体 我们的南卡罗来纳州正在出现关注。这是一个严重的公共卫生威胁，因为有一个 这些新变体可能会逃脱最近开发的Covid-19疫苗或感染的真正风险 以前暴露的个人。这个测序项目将为急需的见识和指导提供 告知我们地区和其他地方的政策决策，以帮助减轻这些潜在威胁。 在2020年秋季，CU建立了新的CLIA认证的Clemson研究和疾病诊断和教育 干预（REDDI）实验室。这已成为该国强大的Covid-19测试计划之一， Reddi实验室测试所有大学人员和学生至少每周一次，其高度准确 Saliva Covid-19 RT-PCR测试，由Clemson的研究人员开发和验证，不久之后 大流行。该实验室还为周围的Upstate SC社区的成员提供免费测试。它处理 在24小时内进行99.9％的测试，目前平均每周超过20,000次测试，其中很大一部分 在该州进行测试。 我们提出以下目标： 目标1：实现SARS-COV2基因组测序工作流和数据收集系统以使用大型 在南卡罗来纳州北部农村建立了Covid-19测试计划。 AIM 2：确定SARS-COV2基因组变体与人口人群，爆发的关联 事件，COVID-19症状严重程度和持续时间，先前的感染和疫苗接种。 鉴于Reddi实验室和最先进的克莱姆森大学基因组学的能力以及 生物信息学设施（CUGBF），理想情况下，我们可以构建一个强大而有益的测序 监视计划。由于靠近主要的旅行枢纽（夏洛特 /亚特兰大），以及 大学人群，许多变体可能会出现在我们的测试池中。更重要的是，我们将捕获数据 来自其他实验室在医院和公共卫生中被其他实验室采样不足的患者人口组 机构。与许多同事测试计划不同，我们实验室检测到的大多数阳性案例是 在诊断时无症状或最小症状的年轻患者（学生）中。在 此外，克莱姆森公共卫生计划与我们的测试实验室合作包括免费的每日测试 社区使用克莱姆森市和一辆移动测试货车的社区，该货车提供宣传 北部地区的处境不利区域不容易获得Covid-19测试。我们的社区测试 人口是上州SC人群的极好代表，包括大量 来自已知COVID-19结果差异的人群的患者。