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)

来自新罕布什尔州大规模校园测试和全州社区的 SARS-CoV-2 全基因组测序——综合生物医学和生物工程研究中心 (CIBBR)

• 批准号: 10381231
• 负责人: Rick H Cote
• 金额: $ 75.71万
• 依托单位: UNIVERSITY OF NEW HAMPSHIRE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381231
• 关键词: 2019-nCoV; Age; Appearance; Area; Biomedical Engineering; COVID-19; COVID-19 pandemic; COVID-19 severity; COVID-19 surveillance; Characteristics; Clinical; Communities; Contact Tracing; Deposition; Diagnostic tests; Disease; Disease Outbreaks; Exhibits; Genbank; Gender; Genomics; Health system; Herd Immunity; Hospitals; Human; Immune system; Immunity; Immunization Programs; Incidence; Individual; Infection; Knowledge; Laboratories; Large-Scale Sequencing; Measures; Metadata; Molecular Diagnostic Testing; New Hampshire; Phase; Population; Population Characteristics; Predisposition; Prevalence; Public Health; Recording of previous events; Research; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 genome; SARS-CoV-2 infection; SARS-CoV-2 variant; Sample Size; Sampling; Sequence Analysis; Severities; Severity of illness; Specimen; Symptoms; Testing; United States Dept. of Health and Human Services; Universities; Vaccinated; Vaccination; Variant; Viral; Viral Load result; Virus; age group; base; community living; disorder risk; experience; genome sequencing; infection rate; novel; racial and ethnic; response; study population; transmission process; variants of concern; whole genome

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.

项目概要/摘要 Covid-19 大流行给全世界的公共卫生系统带来了挑战。十月以来 2020 年，SARS-CoV-2 病毒的新变种已被发现，并且似乎是一个重要的 关注感染率、疾病严重程度以及对先前感染的不同反应的可能性 和/或疫苗接种。在美国，尤其是新罕布什尔州，SARS-CoV-2 的数量 已测序的基因组很少。此外，SARS-CoV-2 测序工作主要是 针对有症状的个体和/或特殊病例的接触者追踪（例如医院传播）。 我们目前缺乏几个领域的知识，包括时间序列和地理定位 区域社区中出现 SARS-CoV-2 变种；病毒事件之间的相关性 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）由特定的 SARS-CoV-2 变体决定。此外，随着美国进入关键时期 在 SARS-CoV-2 大流行阶段，通过预先感染和疫苗接种来建立群体免疫力 计划中，我们也缺乏对先前感染和/或接种疫苗的个人的了解程度 仍然容易受到 SARS-CoV-2 感染，如果是的话，哪些变体正在感染这些所谓的“受保护” 个人。 该项目的目标是确定绝大多数 SARS 病毒的基因组序列 在新罕布什尔州感染者中发现了 CoV-2 变异体，并将这些知识应用于更好的 了解所关注的 SARS-CoV-2 变体增加病毒传播性的可能性，避免 先前感染者的免疫系统，或导致感染者更有可能 经历临床症状。该项目的研究人群包括 12,000 名储存的人类 先前经诊断测试确认含有 SARS-CoV-2 病毒的样本，以及新近发现的样本 在项目期间发现感染 SARS-CoV-2 的样本。 初步全基因组测序结果记录了存储样本的质量以及能力 确定 UNH 聚集社区和社区中存在的 SARS-CoV-2 变种的谱系 一般 NH 人群。 SARS-CoV-2 的大规模基因组监测将允许关联 SARS-CoV-2 具有可用元数据的变异流行率（例如感染日期、地理位置、爆发的严重程度、 症状学和样本人群的特征。 了解 SARS-CoV-2 变种的分布和传染性将为公共卫生提供帮助 拥有有关需要制定的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 变体类型来控制 COVID-19，包括那些 在聚集社区和以前感染过的个体中。