SARS-CoV-2 whole genome sequencing from large-scale campus testing and state-wide communities in NH--Center of Integrated Biomedical and Bioengineering Research (CIBBR)

项目总结/摘要 2019冠状病毒病疫情对全球公共卫生系统构成挑战。了建国以来我党 2020年，SARS-CoV-2病毒的新型变异被发现，似乎是一个重要的 关注感染率、疾病严重程度和对既往感染的可变反应的可能性 和/或疫苗接种。在美国，特别是在新罕布什尔州， 基因组测序一直很稀少。此外，SARS-CoV-2测序工作主要是 针对有症状的个人和/或特殊病例的接触者追踪（例如，医院传播）。 我们目前在几个领域缺乏知识，包括时间顺序和地理位置的 SARS-CoV-2变异体在区域社区的出现;病毒感染事件之间的相关性 疫情和SARS-CoV-2变种;以及种族、民族、性别和年龄对感染的易感性（以及 COVID-19症状的严重程度）。此外，随着美国进入一个关键的 SARS-CoV-2大流行的阶段，通过先前的感染和疫苗接种形成群体免疫力 我们也缺乏对以前感染和/或接种疫苗的人在多大程度上受到感染的了解。 仍然容易受到SARS-CoV-2的感染，如果是这样的话，是什么变种感染了这些所谓的“保护” 个体 该项目的目标是确定大部分SARS病毒的基因组序列， 在NH状态的感染个体中鉴定出CoV-2变异，并将这些知识应用于更好地 了解SARS-CoV-2变异增加病毒传播能力的可能性，避免 以前感染者的免疫系统，或导致感染者更有可能 出现临床症状。本项目的研究人群包括12，000名储存的人类 先前经诊断测试证实含有SARS-CoV-2病毒的标本，以及新的 在项目期间获得的已识别出感染SARS-CoV-2的标本。 初步的全基因组测序结果记录了储存标本的质量以及 为了确定UNH聚集群体中存在的SARS-CoV-2变体的谱系， 一般的人口。SARS-CoV-2的大规模基因组监测将允许SARS-CoV-2相关性 具有可用元数据的变异流行率（例如，感染日期、地理位置、疫情严重程度， 生物学和样本人群的特征。 了解SARS-CoV-2变异体的分布和传染性将为公共卫生提供 需要制定公共卫生措施的更准确和具体信息的机构， 根据特定人群中存在的SARS-CoV-2变异类型控制COVID-19，包括那些 在聚集的社区和以前感染的个人。

PROJECT SUMMARY/ABSTRACT The Covid-19 pandemic has challenged public health systems throughout the world. Since October 2020, novel variants of concern of the SARS-CoV-2 virus have been identified and appear to be a significant concern for rates of infection, severity of disease, and the potential for variable responses to prior infection and/or vaccination. In the US—and especially in the state of New Hampshire—the number of SARS-CoV-2 genomes sequenced has been sparse. Furthermore, SARS-CoV-2 sequencing efforts have primarily been directed toward symptomatic individuals and/or contact tracing of special cases (e.g., hospital transmission). We currently lack knowledge in several areas including the temporal sequence and geolocation of the appearance of SARS-CoV-2 variants in regional communities; the correlation between incidents of viral outbreaks and SARS-CoV-2 variants; and the racial, ethnic, gender, and age susceptibility to infection (and severity of COVID-19 symptoms) by specific SARS-CoV-2 variants. In addition, as the U.S. enters a critical phase of the SARS-CoV-2 pandemic to develop herd immunity through prior infection and the vaccination program, we also lack an understanding of to what extent previously infected and/or vaccinated individuals are still susceptible to infection by SARS-CoV-2, and if so, what variants are infecting these supposedly “protected” individuals. The objective of this project is to determine the genomic sequence of a large majority of the SARS- CoV-2 variants identified in infected individuals in the state of NH and to apply this knowledge to better understand the likelihood that SARS-CoV-2 variants of concern increase the transmissibility of the virus, evade the immune systems of those previously infected, or result in a greater likelihood of infected individuals to experience clinical symptoms. The study population for this project consists of 12,000 stored human specimens previously confirmed by diagnostic tests to contain the SARS-CoV-2 virus, as well as newly identified specimens infected with SARS-CoV-2 as they become available during the project period. Preliminary whole-genome sequencing results document the quality of stored specimens as well as the ability to determine the lineage of SARS-CoV-2 variants present in the UNH congregate community and in the general NH population. Large-scale genomic surveillance of SARS-CoV-2 will permit correlating SARS-CoV-2 variant prevalence with available metadata (e.g., date of infection, geolocation, severity of outbreaks, symptomology, and characteristics of the sample population. Understanding the distribution and infectivity of SARS-CoV-2 variants will provide public health agencies with more accurate and specific information on public health measures that need to be enacted to control COVID-19 based on the types of SARS-CoV-2 variants present in specific populations, including those in congregate communities and previously infected individuals.