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

基本信息

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
项目类别：
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

项目摘要

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.

抽象的提供全面的生物医学信息是国家图书馆使命的核心医学和疾病预防的关键，以实现国内和全球更好的健康结果。传染病预防、实时和无偏见的序列数据对于早期发现至关重要该提议的研究项目旨在减轻疫情、流行病和流行病的威胁。通过利用与传染原相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) 的潜在变革工具 WBE 方法采用分析。对来自大量人口的社区废水进行非侵入性、近乎实时的监测当与高通量宏基因组测序相结合时，有症状和无症状的个体。 (HTS)，由此产生的 WBE-HTS 方法有望用于检测广泛的传染源同时，没有任何关于病毒身份或存在的先验假设，该项目将测试假设对美国可检测到的病毒的聚合宏基因组序列数据进行处理废水可以用于及早发现脆弱性、爆发和流行病，从而创造一种新颖且有效的方法。保护公众健康的潜在挽救生命的诊断方法。为了进行假设检验，该团队将利用亚利桑那州立大学的人类健康观测站（HHO），全球最大的污水监测网络和最大的污水和污泥样本档案库，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一个广泛适用的在线生物信息学框架并在使用 WBE 和 HTS 的案例研究中展示其实用性。这三个具体目标是：(i) 在综合数据库中盘点美国现有的病毒，使用现有数据库源和 WBE；(ii) 生成宏基因组知识库和在线门户数据支持对人类相关病毒组的近实时监测，以及（iii）评估该方法的实用性用于跟踪病毒爆发和流行病的 WBE 生物信息学框架。该项目的成功完成将为美国提供病原体预警系统检测和疫情追踪有助于预防流行病，从而降低发病率和死亡率在美国，来自传染性病原体，首先是病毒，未来可能是致病细菌和其他生物危害。

项目成果

期刊论文数量（16）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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
影响因子：
0
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
作者：
通讯作者：

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.