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.

项目概要/摘要 SARS-CoV-2 大流行给全球公共卫生系统带来了挑战。几个值得关注的变体 已被确定，其中一些会增加传播性、疾病的严重程度、再感染的风险，和/或 对先前感染或疫苗接种的不同反应。在美国，尤其是在新罕布什尔州，这个数字 已测序的 SARS-CoV-2 基因组数量一直很少，但通过我们之前的研究已大幅增加 努力。此外，SARS-CoV-2 测序工作主要针对有症状的患者 个人和/或特殊病例的接触者追踪。我们目前在以下几个方面缺乏知识：（1） 区域社区中 SARS-CoV-2 变种出现的时间顺序和地理定位； (2) 传播性增加与 SARS-CoV-2 变体之间的相关性； (3) 差异 变异在不同种族、民族、性别和年龄组之间的分布以及表现形式 临床症状； (4) 先前感染和/或接种过疫苗的个体获得病毒的程度 病毒以及哪些变种正在重新感染这些人。此外，废水中 SARS-CoV-2 的监测 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 人类样本中的变异以及在同一地理位置的废水样本中检测到的变异。 主要目标是继续确定大量具有代表性的基因组序列 NH 州内的 SARS-CoV-2 变异体并应用这些知识来更好地了解可能性 特定变体增加了病毒的传播能力，逃避了先前病毒的免疫系统 感染，或增加感染者出现临床症状的可能性。我们的中央 假设 SARS-CoV-2 变体的全基因组序列分析将表现出显着差异 在时间和地理位置上的患病率，亚人群被感染和发展的易感性 症状以及感染免疫系统先前受到挑战的个体的能力。 我们将对约 5000 个存档和前瞻性收集的 SARS-CoV-2 诊断样本进行测序 新罕布什尔大学、新罕布什尔州健康与人类部检测呈阳性的个人 达特茅斯学院和达特茅斯的服务以及 COVID-19 监测和临床测试项目- 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 样本作为聚集社区中 SARS-CoV-2 爆发的哨兵，其中直接 可以在来自同一地理位置的废水样本和人体样本之间建立相关性。 了解 SARS-CoV-2 变种的分布和传染性将使公共卫生机构能够 就需要制定的控制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。