Monitoring community health through wastewater based epidemiology: a new analytical framework & technological approaches towards community infectious

全标题：通过基于废水的流行病学监测社区健康：一种新的社区传染病诊断分析框架和技术方法。该项目旨在开发新的分析技术，以帮助验证传染病在城市环境中的传播。可以通过分析废水中的致病RNA来监测疾病的传播吗？为了维持城市健康，迫切需要对城市环境中的公共卫生风险进行快速识别和管理。在我们的团队和更广泛的网络(RENEW和RESTUST、EU INTERWASTE、EU SCORE)中，我们正在开发一个通过城市水指纹识别的尖端、基于证据的公共卫生诊断平台(PHDP)。我们假设，来自城市住宅的水反映了贡献人口的健康状况，因为它汇集了这些人口的内源和外源产品。对这些社区衍生产品(生物标志物)的实时时空测量能够快速评估公共卫生状况，预测未来的危机，并使城市应激源甚至在其表现出特有的终点(例如，传染病流行时的死亡率)之前就能够实施缓解战略。质谱学是鉴定和定量水中化学代谢标志物的首选方法。然而，实现疾病遗传标记量化的历史性突破尚未实现。我们最初将重点关注诺沃克病毒，可能还会关注结核病。将通过以下目标利用英格兰西南部2到3个城市废水处理厂的废水样本来实现这一点：1.在社区一级开发新的传染病诊断分析框架：对传染病进行采样、样品制备、直接聚合酶链式反应。数据分析和统计方法(包括与威塞克斯水务公司密切合作，在信托基金内收集数据)--建立疾病暴发预警系统。低成本、实时识别疾病暴发的新技术方法。这可能包括开发新的CRISPR和基于电化学的检测方法。新的物理科学方法：-开发一种用于制备和分析废水样本的方法学，用于通过dPCR定量RNA。-开发未来的生物传感器方法学(CRISPR/电化学)。学生将做什么：-对于诺沃克病毒和冠状病毒：分析英国公共卫生的数据，以确定适当的目标病原体基因。-对于诺沃克病毒：通过基因测序分析废水中诺沃克病毒的遗传变异性。-为诺沃克病毒和冠状病毒：建立目标病原体基因的dPCR的动态范围。-为废水中的致病核糖核酸开发样本制备和稳定的样本存储方法。-在1-3个地点收集诺沃克病毒和冠状病毒浓度的初始数据。-为未来的生物传感器方法(CRISPR/电化学)启动定期(每周/每月)废水样本收集、准备、存储和分析。-建造生物传感器。-通过检测合成废水中的目标基因，为生物传感器收集概念数据。

Full title: Monitoring community health through wastewater based epidemiology: a new analytical framework and technological approaches towards community infectious disease diagnostics.This project will aim to develop new analysis technologies to help with verification of infectious disease spread in urban environment.Can the spread of disease be monitored through the analysis of wastewater for the pathogenic RNA? Rapid identification and management of public health risks in urban environments are urgently needed to sustain city health. In our group and wider networks (ReNEW and ENTRUST, EU INTERWASTE, EU SCORE) we are developing a cutting-edge, evidence based public health diagnostics platform (PHDP) via urban water fingerprinting. We postulate that water from urban dwellings reflects the health status of contributing population as it pools the endo- & exogenous products of that population. Real-time spatiotemporal measurement of these community derived products (biomarkers) allows for rapid evaluation of public health status, prediction of future crises, and enables mitigation strategies for city's stressors, even before they manifest themselves with characteristic endpoints (e.g. mortality in the event of infectious disease epidemics). Mass spectrometry is the method of choice for chemical metabolic markers identification and quantification in water. However, the historical breakthrough allowing for quantification of genetic markers of disease is yet to be achieved. We will initially focus on norovirus and possibly on TB. This will be achieved using waste water sampled from waste water treatment plants in 2 or 3 cities in South West England via the following objectives:1. Development of a new analytical framework for infectious disease diagnostics at the community-level: sampling, sample prep, dPCR for infectious disease.2. Data analysis and statistical approaches (incl. data collected within ENTRUST in close collaboration with Wessex Water) - towards early warning system for disease outbreak.3. New technological approaches for low cost and real time identification of disease outbreak. This might include the development of novel CRISPR and electrochemistry-based detection methodologies.Novel physical sciences methodology:- Development of a methodology for the preparation and analysis of wastewater samples for RNA quantification by dPCR.- Development of a future biosensor methodology (CRISPR/electrochemistry).What will the student be doing:-For both norovirus and coronavirus: analysing Public Health England data to determine the appropriate target pathogen gene. -For norovirus: analysing the genetic variability of norovirus in wastewater by gene sequencing. -For both norovirus and coronavirus: establishing the dynamic range of dPCR for the target pathogen gene.-Developing a sample preparation and stable sample storage methodology for pathogenic RNA from wastewater.-Gathering initial data for norovirus and coronavirus concentration in 1-3 locations.-Initiating regular (weekly/monthly) wastewater sample collection, preparation, storage and analysis for a future biosensor methodology (CRISPR/electrochemistry).-Building that biosensor.-Gathering proof of concept data for the biosensor via the detection of the target gene in synthetic waste water.