SARS-CoV-2 whole genome sequencing from large-scale campus testing and state-wide communities in NH

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

• 批准号: 10595370
• 负责人: Rick H Cote
• 金额: $ 78.92万
• 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/10595370
• 关键词: 2019-nCoV; Appearance; Archives; Area; Biological; COVID-19; COVID-19 diagnostic; COVID-19 outbreak; COVID-19 pandemic; COVID-19 surveillance; COVID-19 testing; Centers of Research Excellence; Clinical; Collaborations; Communities; Contact Tracing; Data; Deposition; Epidemiology; Evaluation; Exhibits; Funding; Future; Genbank; Gender; Genomics; Health; Health system; Hospitals; Human; Immune system; Individual; Infection; Knowledge; Laboratories; Large-Scale Sequencing; Link; Measures; Medical center; Medicine; Metadata; Molecular Diagnostic Testing; New Hampshire; Outcome; Pathology; Persons; Population; Predisposition; Prevalence; Protocols documentation; Public Health; Research; Research Personnel; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2 genome; SARS-CoV-2 variant; Sampling; Sentinel; Sequence Analysis; Severity of illness; Source; Specimen; Symptoms; System; Testing; United States Dept. of Health and Human Services; Universities; Vaccination; Vaccinee; Variant; Viral; Virus; Work; age group; base; college; data sharing; demographics; disorder risk; experience; genome sequencing; insight; novel; programs; prospective; racial and ethnic; research clinical testing; response; tool; transmission process; variants of concern; wastewater samples; wastewater surveillance; whole genome

PROJECT SUMMARY/ABSTRACT The SARS-CoV-2 pandemic has challenged public health systems globally. Several variants of concern have been identified, some of which increase transmissibility, severity of disease, risk for reinfection, and/or variable responses to prior infection or vaccination. In the US—and especially in New Hampshire—the number of SARS-CoV-2 genomes sequenced has been sparse but have been substantially increased by our prior efforts. Furthermore, SARS-CoV-2 sequencing efforts have primarily been directed toward symptomatic individuals and/or contact tracing of special cases. We currently lack knowledge in several areas: (1) the temporal sequence and geolocation of the appearance of SARS-CoV-2 variants in regional communities; (2) the correlation between increases in transmissibility and SARS-CoV-2 variants; (3) differences in the distribution of variants among different racial, ethnic, gender, and age groups as well as in presentation of clinical symptoms; and (4) the extent to which previously infected and/or vaccinated individuals acquire the virus and which variants are reinfecting these individuals. In addition, wastewater surveillance of SARS-CoV-2 is a valuable public health tool but we lack an understanding of the relationship between the SARS-CoV-2 variants in human specimens and the variants detected in wastewater samples from the same geolocation. The primary objective is to continue determining the genomic sequence of a large, representative set of SARS-CoV-2 variants within the state of NH and to apply this knowledge to better understand the likelihood that specific variants increase transmissibility of the virus, evade the immune systems of those previously infected, or increase the likelihood of infected individuals to experience clinical symptoms. Our central hypothesis is that whole genome sequence analysis of SARS-CoV-2 variants will exhibit significant differences in temporal and geolocation prevalence, susceptibility of sub-populations to become infected and develop symptoms, and ability to infect individuals whose immune systems have previously been challenged. We will sequence ~5000 archived and prospectively collected SARS-CoV-2 diagnostic specimens from individuals who test positive from the University of New Hampshire, the NH Department of Health and Human Services, and the COVID-19 surveillance and clinical testing programs at Dartmouth College and Dartmouth- Hitchcock Medical Center. In addition, we will evaluate the ability of genomic surveillance of wastewater samples to serve as a sentinel for SARS-CoV-2 outbreaks in a congregate community where direct correlations can be made between wastewater samples and human specimens from the same geolocation. Understanding the distribution and infectivity of SARS-CoV-2 variants will enable public health agencies to provide more accurate and specific guidance 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.

项目摘要/摘要 SARS-COV-2大流行对全球公共卫生系统提出了挑战。几种关注的变体 已经确定了，其中一些增加了传播，疾病的严重程度，再感染风险和/或 对先前感染或疫苗接种的可变反应。在美国，尤其是在新罕布什尔州，这个数字 测序的SARS-COV-2基因组稀疏，但我们先前已经大大增加了 努力。此外，SARS-COV-2测序工作主要针对症状 特殊情况的个人和/或接触跟踪。我们目前在多个领域缺乏知识：（1） SARS-COV-2变体在区域社区中的临时顺序和地理位置； （2） 传输与SARS-COV-2变体的增加之间的相关性； （3）差异 不同种族，种族，性别和年龄段之间的变体分布以及呈现 临床症状； （4）先前感染和/或接种人获得的程度 病毒和哪些变体正在恢复这些人。此外，SARS-COV-2的废水监视 是一种有价值的公共卫生工具，但我们对SARS-COV-2之间的关系缺乏了解 人类标本中的变体和从相同地理位置的废水样品中检测到的变体。 主要目的是继续确定大型代表性集的基因组序列 NH状态内的SARS-COV-2变体并运用这些知识以更好地了解可能性 该特定变体增加了病毒的传播，逃避了以前的人的免疫系统 感染或增加感染个体经历临床症状的可能性。我们的中心 假设是SARS-COV-2变体的整个基因组序列分析将暴露出显着差异 在暂时和地理位置的患病率中，亚群体被感染和发展的敏感性 症状和感染免疫系统以前受到挑战的人的能力。 我们将对〜5000个存档并前瞻性地收集的SARS-COV-2诊断标本对 来自新罕布什尔大学，新罕布什尔州卫生与人类的个人测试阳性的个人 服务，以及达特茅斯学院和达特茅斯 - 希区柯克医疗中心。此外，我们将评估废水基因组监测的能力 在一个聚会社区中作为SARS-COV-2爆发的哨兵的样本 可以从相同的地理位置中的废水样品和人类标本之间建立相关性。 了解SARS-COV-2变体的分布和感染将使公共卫生机构能够 为需要制定的公共卫生措施提供更准确和具体的指导 COVID-19基于特定人群中存在的SARS-COV-2变体类型。