Bioinformatics Framework for Wastewater-based Surveillance of Infectious Diseases

基于废水的传染病监测的生物信息学框架

• 批准号: 10575463
• 负责人: ROLF U HALDEN
• 金额: $ 46.66万
• 依托单位: ARIZONA STATE UNIVERSITY-TEMPE CAMPUS
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-03 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10575463
• 关键词: Archives; Area; Arizona; Biohazardous Substance; Bioinformatics; Biotechnology; Caring; Case Study; Centers for Disease Control and Prevention (U.S.); Characteristics; Cities; Clinic; Clinical; Communicable Diseases; Communities; DNA Sequence; DNA Viruses; Data; Databases; Detection; Disease; Disease Outbreaks; Early Diagnosis; Environmental Monitoring; Environmental sludge; Epidemic; Equipment and supply inventories; Ethnic Origin; Feces; Foundations; Future; Genbank; Genome; Goals; Health; Health protection; High-Throughput Nucleotide Sequencing; Hospitals; Human; Human poliovirus; Individual; Infectious Agent; Influenza A virus; Institutes; International; Israel; Joints; Laboratories; Life; Medical; Metagenomics; Mission; Monitor; Morbidity - disease rate; Norovirus; Outcome; Pathogen detection; Pathogenicity; Plants; Poliomyelitis; Population; Population Surveillance; Process; Public Health; Publishing; RNA Sequences; RNA Viruses; Reporting; Research; Research Personnel; Research Project Grants; Resources; Rotavirus; Sampling; Savings; Sentinel; Sequence Analysis; Severities; Sewage; Socioeconomic Status; Solid; Source; Specimen; Symptoms; System; Testing; Time; Translating; United States National Library of Medicine; Universities; Viral; Viral Genome; Virion; Virus; Virus Diseases; Water; Work; World Health Organization; base; biomedical informatics; data streams; database design; diagnostic strategy; disorder prevention; frontier; geographic population; innovation; knowledge repository; metagenomic sequencing; microbial genome; mortality; novel; novel virus; pandemic disease; pathogen; pathogenic bacteria; pathogenic virus; population health; preempt; prevent; public health intervention; real time monitoring; sample archive; seasonal influenza; support tools; syndromic surveillance; tool; virome; wastewater epidemiology; wastewater monitoring; wastewater surveillance; web portal

Abstract Enabling access to comprehensive biomedical information is central to the mission of the National Library of Medicine and key to disease prevention for better health outcomes nationally and globally. In the area of infectious disease prevention, real time and non-biased sequence data are essential for early detection of threats to mitigate outbreaks, epidemics and pandemics. This proposed research project aims to innovate in the creation and accessibility of metagenomic sequence data relating to infectious agents by leveraging the potentially transformative tool of wastewater-based epidemiology (WBE). The WBE approach employs analysis of community wastewater from large populations to enable non-invasive, near real-time monitoring of both symptomatic and asymptomatic individuals. When combined with high-throughput metagenomic sequencing (HTS), the resulting WBE-HTS approach is promising for detecting a broad spectrum of infectious agents simultaneously without any a priori assumptions about virus identity or presence. This project will test the hypothesis that the processing of aggregated metagenomic sequence data on viruses detectable in U.S. wastewater can serve to identify vulnerabilities, outbreaks and epidemics early, thereby creating a novel and potentially life-saving diagnostic approach for protecting public health. For hypothesis testing, the team will leverage Arizona State University's Human Health Observatory (HHO), the largest sewage monitoring network and largest archive of sewage and sludge samples worldwide, representing more than 200 U.S. cities and over 300 cities globally. The overall goal of this work is to develop a broadly applicable online bioinformatics framework and to demonstrate its utility in a case study employing WBE and HTS. The three specific aims are to: (i) inventory viruses extant in the U.S. in a comprehensive database, using existing database sources and WBE; (ii) generate a knowledge repository and online portal of metagenomic data to support near real-time surveillance of the human–associated virome, and (iii) evaluate the utility of the WBE bioinformatics framework for tracking viral outbreaks and epidemics. Successful completion of this project will provide the U.S. with an early warning system for pathogen detection and outbreak tracking that can serve to prevent epidemics, thereby reducing morbidity and mortality in the U.S. from contagious pathogens, first for viruses and potentially in the future for pathogenic bacteria and other biohazards.

抽象的 允许访问综合生物医学信息是国家图书馆任务的核心 医学和预防疾病的关键，以改善全国和全球的健康状况。在 预防传染病，实时和非偏置序列数据对于早期检测至关重要 威胁减轻爆发，情节和大流行的威胁。这个拟议的研究项目旨在创新 通过利用与感染剂有关的宏基因组序列数据的创建和可访问性。 基于废水的流行病学（WBE）的潜在变革性工具。 WBE方法员工分析 大量人口的社区废水以实现非侵入性的，几乎实时监测两者 有症状和无症状的个体。当与高通量宏基因组测序结合使用时 （HTS），承诺将最终的WBE-HTS方法检测到广泛的传染剂 同样，没有关于病毒身份或存在的任何先验假设。该项目将测试 假设在美国可检测到的有关病毒的汇总核序列数据处理 废水可以早日识别漏洞，爆发和情节，从而创建小说和 潜在的挽救生命的诊断方法来保护公共卫生。 对于假设检验，该团队将利用亚利桑那州立大学的人类健康天文台（HHO）， 全球最大的污水监测网络和最大的污水和污泥样品档案 代表200多个美国城市和全球300多个城市。 这项工作的总体目标是开发广泛适用的在线生物信息学框架，并 在使用WBE和HTS的案例研究中演示其效用。 这三个具体目的是：（i）美国在美国的库存病毒范围，使用 现有的数据库来源和WBE； （ii）生成元基因组的知识存储库和在线门户 支持人类相关病毒蛋白的近乎实时监视的数据，以及（iii）评估效用 WBE生物信息学框架，用于跟踪病毒爆发和流行病。 该项目的成功完成将为美国提供病原体的预警系统 检测和爆发跟踪可以用于防止发作，从而降低发病率和死亡率 在美国，来自传染病的病原体，首先是病毒，未来可能用于致病细菌和 其他生物危害。

项目成果

Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020.

基于废水的流行病学和长读长测序，以识别 2020 年 6 月至 10 月美国西南部亚利桑那州马里科帕县三个城市的肠道病毒循环。

• DOI: 10.3390/v13091803
• 发表时间: 2021-09-10
• 期刊: Viruses
• 作者: Faleye TOC;Bowes DA;Driver EM;Adhikari S;Adams D;Varsani A;Halden RU;Scotch M
• 通讯作者: Scotch M

Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study.

• DOI: 10.1016/s2666-5247(22)00289-0
• 发表时间: 2023-01
• 期刊: LANCET MICROBE
• 影响因子: 38.2
• 作者: Bowes, Devin A.;Driver, Erin M.;Kraberger, Simona;Fontenele, Rafaela S.;Holland, LaRinda A.;Wright, Jillian;Johnston, Bridger;Savic, Sonja;Newell, Melanie Engstrom;Adhikari, Sangeet;Kumar, Rahul;Goetz, Hanah;Binsfeld, Allison;Nessi, Kaxandra;Watkins, Payton;Mahant, Akhil;Zevitz, Jacob;Deitrick, Stephanie;Brown, Philip;Dalton, Richard;Garcia, Chris;Inchausti, Rosa;Holmes, Wydale;Tian, Xiao-Jun;Varsani, Arvind;Lim, Efrem S.;Scotch, Matthew;Halden, Rolf U.
• 通讯作者: Halden, Rolf U.

Genome Sequences of Anelloviruses, Genomovirus, and Papillomavirus Isolated from Nasal Pharyngeal Swabs.

• DOI: 10.1128/mra.00681-22
• 发表时间: 2022-09-15
• 期刊: Microbiology resource announcements
• 影响因子: 0.8

Coding-Complete Genome Sequence of a Human Respirovirus 1 Strain from a Clinical Sample in Arizona.

来自亚利桑那州临床样本的人类呼吸道病毒 1 株的完整基因组序列编码。

• DOI: 10.1128/mra.00465-20
• 发表时间: 2020
• 期刊: Microbiology resource announcements
• 影响因子: 0.8
• 作者: Scotch,Matthew;Halden,RolfU;Denton,Anthony;Sandrolini,Helen;Fontenele,RafaelaS;Varsani,Arvind
• 通讯作者: Varsani,Arvind

Detection of human, porcine and canine picornaviruses in municipal sewage sludge using pan-enterovirus amplicon-based long-read Illumina sequencing.

• DOI: 10.1080/22221751.2022.2071173
• 发表时间: 2022-12
• 期刊: Emerging microbes & infections
• 影响因子: 13.2