SARS-CoV2 Sequencing Surveillance Program for Upstate South Carolina

项目摘要 该项目的总体目标是继续并扩大监测工作，以发现和监测现有的 通过对广泛的大学监测和检测到的阳性样本进行测序 克莱姆森大学(CU)社区测试项目。SARS-CoV-2病毒的变种引起了巨大的关注 世界范围内的疫情事件。正如我们在南部北部三角洲和奥米克龙重大疫情期间所追踪的那样 卡罗莱纳州，这构成了严重的公共健康威胁；新的变种可以逃脱新冠肺炎的报道 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。 为应对新冠肺炎大流行，CU建立了稳健的高通量新冠肺炎诊断检测 该计划使该大学能够在疫情的大部分时间里保持面对面教学的开放。 CLIA认证的克莱姆森疾病诊断和干预研究和教育(Reddi)实验室拥有 促进对所有大学人员的定期测试，并向周围州北部南部的成员提供免费测试 卡罗莱纳社区。在南卡罗来纳州的所有新冠肺炎检测中，该实验室进行了10%的检测。2021年，雷迪 LAB与加州大学基因组和生物信息学研究所(CUGBF)合作建立SARS-CoV-2基因组学 测序计划，绘制了3个主要疫情事件图，并提供了三角洲和 南卡罗来纳州北部农村地区的奥米克龙变种。这些数据有助于向预警局提供信息 先发制人的新冠肺炎政策和及时的回应，为大学以及北部的南加州城市和直辖市。 此外，测序监测计划允许对变异特异性进行重大的科学发现 疾病表现、疫苗效力的差异和先前的感染保护、监测 测试和新冠肺炎缓解战略，以及废水社区监测工作。结果来自于 测序计划还导致了用于新冠肺炎诊断的新分析方法和技术的开发 监测以及本科生和研究生培训和社区外展计划。 为了实现我们继续监测SARS-CoV-2基因组的总体目标，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、疫情 事件、新冠肺炎症状严重程度和持续时间、既往感染和接种疫苗。 目标2：开发实时工作流和数据分析平台，以应对各种监视的挑战 通过正在进行的新冠肺炎疫情，为其不可避免地从大流行阶段过渡到流行阶段。 在过去的一年里，我们创建了一个独特的、强大的测序程序，不仅对样本进行了测序 而且还将结果与丰富的大学和社区新冠肺炎监控数据库联系起来，以实现安全 和有效的数据挖掘，以进行持续分析。我们的社区测试计划提供了测试和 对北部偏远和服务不足的地区进行监控。这提供了一个很好的表示 南卡罗来纳州北部的人口统计数据，包括来自已知人群的大量患者 新冠肺炎成果差异。由于这所大学和我们靠近主要的旅游枢纽(例如， 亚特兰大/夏洛特)我们地区有大量的旅行者将新的变种引入我们的相对 农村社区。在过去的一年里，我们已经证明了SARS-CoV-2变种在农村地区的流行 南卡罗来纳州北部与该州其他地区截然不同。此外，我们的程序从患者的人口统计数据中获取数据 医院和公共卫生机构的其他实验室高度抽样不足的群体。大多数人 我们实验室发现的阳性病例都是年轻的，通常当时没有症状或症状很轻。 诊断的结果。然而，我们已经证明，特别是在关注的新变种中，这些患者可以 很容易将疾病传播给其他人，而他们自己，即使是轻微的症状，有时也会有更长的时间 对健康有持久的影响。总体而言，这表明需要继续支持SARS-CoV-2测序 研究新冠肺炎在我们地区和我们人口群体中的演变。

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.