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

全文：通过基于废水的流行病学监测社区健康：社区传染病诊断的新分析框架和技术方法。该项目旨在开发新的分析技术，以帮助核实传染病在城市环境中的传播。能否通过分析废水中的致病RNA来监测疾病的传播？为了维持城市健康，迫切需要快速识别和管理城市环境中的公共卫生风险。在我们的集团和更广泛的网络（ReNEW和ENTRUST， EU INTERWASTE, EU SCORE）中，我们正在通过城市水指纹技术开发一个前沿的、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，因为它汇集了该人口的内源性和外源性产品。对这些社区衍生产品（生物标志物）进行实时时空测量，可以快速评估公共卫生状况，预测未来的危机，甚至在城市压力源以特征端点表现出来之前（例如，传染病流行时的死亡率），就可以采取缓解战略。质谱法是鉴定和定量水中化学代谢标志物的首选方法。然而，允许疾病遗传标记量化的历史性突破尚未实现。我们将首先关注诺如病毒，可能还会关注结核病。这将通过使用从英格兰西南部2或3个城市的污水处理厂取样的废水来实现以下目标：1 .为社区一级的传染病诊断制定新的分析框架：传染病的抽样、样品制备、dPCR。2 .数据分析和统计方法（包括与威塞克斯水务公司密切合作，在委托内收集的数据）——用于疾病爆发的早期预警系统。低成本和实时识别疾病暴发的新技术途径。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：-开发了一种方法，用于制备和分析废水样品，通过dPCR进行RNA定量。-开发未来的生物传感器方法（CRISPR/电化学）。学生将做什么：-诺如病毒和冠状病毒：分析英国公共卫生数据，以确定适当的目标病原体基因。-诺如病毒：通过基因测序分析废水中诺如病毒的遗传变异性。-诺如病毒和冠状病毒：建立目标病原体基因dPCR的动态范围。-开发废水致病性RNA的样品制备和稳定的样品储存方法。-收集1-3个地点诺如病毒和冠状病毒浓度的初步数据。-启动定期（每周/每月）废水样品收集，制备，储存和分析，用于未来的生物传感器方法（CRISPR/电化学）。-制造生物传感器。-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证明。

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.