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.

项目摘要/摘要 COVID-19大流行对世界各地的公共卫生系统提出了挑战。自十月以来 2020年，已经确定了SARS-COV-2病毒关注的新型变体，并且似乎很重要 关注感染率，疾病严重程度以及对先前感染的可变反应的潜力 和/或疫苗接种。在美国，尤其是在新罕布什尔州，SARS-COV-2的数量 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/或特殊病例的接触跟踪（例如，医院传播）。 目前，我们在多个领域缺乏知识，包括临时顺序和地理位置 区域社区中SARS-COV-2变体的出现；病毒事件之间的相关性 爆发和SARS-COV-2变体；以及种族，种族，性别和年龄对感染的敏感性（和 COVID-19症状的严重程度）通过特定的SARS-COV-2变体。此外，随着美国进入关键 SARS-COV-2大流行的阶段，通过先前的感染和疫苗接种发展群免疫。 计划，我们还缺乏了解以前感染和/或接种疫苗的人是多大程度上的理解 仍然容易受到SARS-COV-2的感染，如果是的话，这些变体被感染了这些所谓的“受保护” 个人。 该项目的目的是确定绝大多数SARS-的基因组序列 在NH状态下在受感染的个体中鉴定出的COV-2变体，并将这些知识应用于更好 了解SARS-COV-2的关注变体增加病毒的传播，逃避的可能性 先前感染者的免疫系统，或导致感染个体的可能性更大 经历临床症状。该项目的研究人群由12,000个存储的人类组成 先前通过诊断测试确认的标本包含SARS-COV-2病毒，以及新的标本 在项目期间可用时，确定了感染了SARS-COV-2的标本。 初步的全基因组测序结果记录了存储标本的质量以及能力 确定UND聚集社区中存在的SARS-COV-2变体的谱系 一般NH人口。 SARS-COV-2的大规模基因组监视将允许与SARS-COV-2相关 可用元数据的变体患病率（例如，感染日期，地理位置，暴发的严重程度， 症状和样本人群的特征。 了解SARS-COV-2变体的分布和感染将提供公共卫生 具有更准确和具体信息的机构，需要颁布的公共卫生措施 基于特定人群中存在的SARS-COV-2变体的类型，控制Covid-19，包括 在聚集社区和以前感染的个人中。