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: 10691023
• 负责人: Hai Yao
• 金额: $ 67.3万
• 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 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10691023
• 关键词: Advisory Committees; Animal Model; Animal Testing; Animals; Area; Award; Basic Science; Bioinformatics; Biology; Biomedical Engineering; Biomedical Research; Bone Diseases; Cadaver; Centers of Research Excellence; Clinical; Collaborations; Communities; Complement; Computer Models; Data; Development; Devices; Discipline; Evaluation; Faculty; Faculty Recruitment; Fostering; Funding; Future; Glossary; Goals; Health; Health system; Healthcare; Human; Infrastructure; Intervention; Investments; Medical; Medical Research; Medicine; Mentors; Modeling; Modernization; Musculoskeletal; Musculoskeletal Diseases; Musculoskeletal System; Nature; Outcome; Patients; Performance; Personnel Recruitments; Persons; Physics; Precision therapeutics; Private Sector; Process; Public Health; Publishing; Randomized Clinical Trials; Research; Research Infrastructure; Research Personnel; Resources; Schools; Shapes; South Carolina; Specimen; Supercomputing; Systems Biology; Technology; Technology Transfer; Testing; Therapeutic; Therapeutic Intervention; Therapeutic Uses; Time; Tissues; Training; Translating; Translational Research; Translations; United States; United States National Institutes of Health; Universities; Validation; Work; acronyms; aging population; arthropathies; base; body system; career; clinical practice; cluster computing; cost; disability; equipment acquisition; flexibility; improved; in vivo; innovation; interdisciplinary approach; interest; materials science; multi-scale modeling; multidisciplinary; novel; novel strategies; novel therapeutic intervention; pre-clinical assessment; precision medicine; programs; sensor technology; skeletal; success; systems research; technology development; virtual human

Project Summary The overall objective of this project is to continue and expand surveillance efforts to detect and monitor extant and emerging variants by sequencing the positive samples detected by the extensive university surveillance and community testing programs at Clemson University (CU). Variants of concern of SARS-CoV-2 have caused large outbreak events worldwide. As we tracked during the significant Delta and Omicron outbreaks in Upstate South Carolina, this poses a serious public health threat; the new variants can escape the coverage of COVID-19 vaccines or infect previously exposed individuals. Our sequencing surveillance program aims to continue to provide much-needed insight and guidance to inform policy decisions to help mitigate these potential threats. In response to the COVID-19 pandemic, CU established a robust high-throughput COVID-19 diagnostic testing program, which enabled the university to remain opened to in-person instruction through most of the pandemic. The CLIA-certified Clemson Research and Education in Disease Diagnosis and Intervention (REDDI) Lab has facilitated regular testing of all university personnel and free testing to members of the surrounding Upstate South Carolina community. The lab has run >10% of all the COVID-19 tests from South Carolina. In 2021, the REDDI Lab partnered with the CU Genomics and Bioinformatic Facility (CUGBF) to set up a SARS-CoV-2 genomics sequencing program, which mapped 3 major outbreak events and provided early detection of the Delta and Omicron variants in the rural Upstate South Carolina region. These data were instrumental to inform the pre- emptive COVID-19 policies and timely response for the university as well as Upstate SC cities and municipalities. In addition, the sequencing surveillance program allowed for significant scientific discovery on variant specific disease presentation, variant differences in effectiveness of vaccine and prior infection protection, surveillance testing and COVID-19 mitigation strategies, and wastewater community surveillance efforts. The results from the sequencing program also led to the development of new assays and technologies for COVID-19 diagnosis and surveillance as well as undergraduate and graduate student training and community outreach programs. To accomplish our overall goals of continued SARS-CoV-2 genomic surveillance, we propose the following aims: Aim 1: Determine the association of SARS-CoV-2 genomic variants with population demographics, outbreak events, COVID-19 symptom severity and duration, previous infection, and vaccination. Aim 2: Develop real-time workflows and data analytics platforms to meet the challenge of variant surveillance through the on-going COVID-19 situation for its inevitable transition from pandemic to endemic phase. Over the last year, we have created a unique and robust sequencing program that not only sequences samples but also ties the results to a rich university and community COVID-19 surveillance database to enable secure and effective data mining for continued analysis. Our community testing program has provided testing and surveillance to remote and underserved areas of the Upstate. This provided for an excellent representation of the Upstate South Carolina demographics, including significant numbers of patients from populations with known COVID-19 outcome disparities. Because of the university and our proximity to major travel hubs (e.g., Atlanta/Charlotte) there is significant flux of travelers in our area who introduce new variants into our relatively rural community. Over the past year, we have demonstrated that the SARS-CoV-2 variant prevalence in rural Upstate SC is distinct from the rest of the state. In addition, our program captured data from patient demographic groups that are highly under-sampled by other labs at hospitals and public health agencies. The majority of positive cases detected by our lab were young and usually asymptomatic or minimally symptomatic at the time of diagnosis. However, we have shown that, particularly with the newer variants of concern, these patients can readily spread the disease to others and they, themselves, even with mild symptoms, can sometimes have longer lasting health effects. Overall, this has demonstrated the need for continued SARS-CoV-2 sequencing support to study the evolving COVID-19 pandemic in our region and for our population groups.

项目摘要 该项目的总体目标是继续并扩大监测工作， 通过对广泛的大学监测检测到的阳性样本进行测序， 克莱姆森大学（CU）的社区测试项目。SARS-CoV-2的变异引起了大量的关注， 全球爆发事件。正如我们在南部北部的三角洲和奥米克戎爆发期间所追踪的那样 在卡罗莱纳，这构成了严重的公共卫生威胁;新的变种可以逃脱COVID-19的覆盖范围 疫苗或感染以前接触过的人。我们的测序监测计划旨在继续 提供急需的洞察力和指导，为政策决策提供信息，以帮助缓解这些潜在威胁。 为应对COVID-19疫情，中大建立了强大的高通量COVID-19诊断检测 该计划使该大学能够在大流行期间的大部分时间内保持对面对面教学的开放。 CLIA认证的克莱姆森疾病诊断和干预研究和教育（REDDI）实验室 促进了所有大学人员的定期测试和免费测试，以周围的北部南部的成员 卡罗莱纳社区。该实验室已经运行了来自南卡罗来纳州的所有COVID-19测试的10%以上。2021年，REDDI 实验室与CU基因组学和生物信息学设施（CUGBF）合作，建立了SARS-CoV-2基因组学 测序计划，该计划绘制了3个主要爆发事件，并提供了三角洲的早期检测， 南卡罗来纳州北部农村地区的奥密克隆变种。这些数据有助于告知前- 积极的COVID-19政策和及时的反应，为大学以及北南卡罗来纳州的城市和市政当局。 此外，测序监测计划允许在变异特异性上的重大科学发现。 疾病表现、疫苗有效性和既往感染保护的变异差异、监测 测试和COVID-19缓解策略，以及废水社区监测工作。的结果 测序计划还导致了新的COVID-19诊断方法和技术的发展 以及本科生和研究生培训和社区外展计划。 为了实现我们持续SARS-CoV-2基因组监测的总体目标，我们提出了以下目标： 目的1：确定SARS-CoV-2基因组变异与人口统计学特征、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。 目标2：开发实时工作流程和数据分析平台，以应对变异监测的挑战 持续的2019冠状病毒病疫情不可避免地从大流行阶段过渡到地方流行阶段。 在过去的一年里，我们创建了一个独特而强大的测序程序，不仅可以对样本进行测序， 而且还将结果与丰富的大学和社区COVID-19监测数据库联系起来， 和有效的数据挖掘进行持续分析。我们的社区测试计划提供了测试和 监控到偏远和服务不足的地区北部。这是一个很好的代表性， 南卡罗来纳州北部的人口统计学数据，包括来自已知 COVID-19结果差异。由于大学和我们靠近主要的旅游中心（例如， 亚特兰大/夏洛特）在我们地区有大量的旅行者，他们将新的变体引入我们相对 农村社区。在过去的一年里，我们已经证明了SARS-CoV-2变异在农村的流行， 上州SC与该州其他地区不同。此外，我们的程序从患者人口统计学中获取数据， 医院和公共卫生机构的其他实验室对这些群体的抽样严重不足。大多数 我们实验室检测到的阳性病例都是年轻人，当时通常没有症状或症状轻微 诊断。然而，我们已经证明，特别是对于新的变异，这些患者可以 很容易将疾病传播给他人，他们自己，即使症状轻微，有时也会有更长的时间 持久的健康影响。总的来说，这表明需要持续的SARS-CoV-2测序支持 研究我们地区和我们人群中不断演变的COVID-19大流行。