A spatio-temporal framework for modelling wastewater concentration during the COVID-19 pandemic

Analysis insights to support the use of wastewater and environmental surveillance data for infectious diseases and pandemic preparedness

Wastewater-based epidemiology is the detection of pathogens from sewage systems and the interpretation of these data to improve public health. Its use has increased in scope since 2020, when it was demonstrated that SARS-CoV-2 RNA could be successfully extracted from the wastewater of affected populations. In this Perspective we provide an overview of recent advances in pathogen detection within wastewater, propose a framework for identifying the utility of wastewater sampling for pathogen detection and suggest areas where analytics require development. Ensuring that both data collection and analysis are tailored towards key questions at different stages of an epidemic will improve the inference made. For analyses to be useful we require methods to determine the absence of infection, early detection of infection, reliably estimate epidemic trajectories and prevalence, and detect novel variants without reliance on consensus sequences. This research area has included many innovations that have improved the interpretation of collected data and we are optimistic that innovation will continue in the future.

Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey

The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.

Wastewater-based Epidemiology for COVID-19 Surveillance and Beyond: A Survey

The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.

Advancing Public Health Surveillance: Integrating Modeling and GIS in the Wastewater-Based Epidemiology of Viruses, a Narrative Review

This review article will present a comprehensive examination of the use of modeling, spatial analysis, and geographic information systems (GIS) in the surveillance of viruses in wastewater. With the advent of global health challenges like the COVID-19 pandemic, wastewater surveillance has emerged as a crucial tool for the early detection and management of viral outbreaks. This review will explore the application of various modeling techniques that enable the prediction and understanding of virus concentrations and spread patterns in wastewater systems. It highlights the role of spatial analysis in mapping the geographic distribution of viral loads, providing insights into the dynamics of virus transmission within communities. The integration of GIS in wastewater surveillance will be explored, emphasizing the utility of such systems in visualizing data, enhancing sampling site selection, and ensuring equitable monitoring across diverse populations. The review will also discuss the innovative combination of GIS with remote sensing data and predictive modeling, offering a multi-faceted approach to understand virus spread. Challenges such as data quality, privacy concerns, and the necessity for interdisciplinary collaboration will be addressed. This review concludes by underscoring the transformative potential of these analytical tools in public health, advocating for continued research and innovation to strengthen preparedness and response strategies for future viral threats. This article aims to provide a foundational understanding for researchers and public health officials, fostering advancements in the field of wastewater-based epidemiology.

Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater

Wastewater surveillance has proven a cost-effective key public health tool to understand a wide range of community health diseases and has been a strong source of information on community levels and spread for health departments throughout the SARS- CoV-2 pandemic. Studies spanning the globe demonstrate the strong association between virus levels observed in wastewater and quality clinical case information of the population served by the sewershed. Few of these studies incorporate the temporal dependence present in sampling over time, which can lead to estimation issues which in turn impact conclusions. We contribute to the literature for this important public health science by putting forward time series methods coupled with statistical process control that (1) capture the evolving trend of a disease in the population; (2) separate the uncertainty in the population disease trend from the uncertainty due to sampling and measurement; and (3) support comparison of sub-sewershed population disease dynamics with those of the population represented by the larger downstream treatment plant. Our statistical methods incorporate the fact that measurements are over time, ensuring correct statistical conclusions. We provide a retrospective example of how sub-sewersheds virus levels compare to the upstream wastewater treatment plant virus levels. An on-line algorithm supports real-time statistical assessment of deviations of virus level in a population represented by a sub-sewershed to the virus level in the corresponding larger downstream wastewater treatment plant. This information supports public health decisions by spotlighting segments of the population where outbreaks may be occurring.

Integrating wastewater and randomised prevalence survey data for national COVID surveillance

During the COVID-19 pandemic, studies in a number of countries have shown how wastewater can be used as an efficient surveillance tool to detect outbreaks at much lower cost than traditional prevalence surveys. In this study, we consider the utilisation of wastewater data in the post-pandemic setting, in which collection of health data via national randomised prevalence surveys will likely be run at a reduced scale; hence an affordable ongoing surveillance system will need to combine sparse prevalence data with non-traditional disease metrics such as wastewater measurements in order to estimate disease progression in a cost-effective manner. Here, we use data collected during the pandemic to model the dynamic relationship between spatially granular wastewater viral load and disease prevalence. We then use this relationship to nowcast local disease prevalence under the scenario that (i) spatially granular wastewater data continue to be collected; (ii) direct measurements of prevalence are only available at a coarser spatial resolution, for example at national or regional scale. The results from our cross-validation study demonstrate the added value of wastewater data in improving nowcast accuracy and reducing nowcast uncertainty. Our results also highlight the importance of incorporating prevalence data at a coarser spatial scale when nowcasting prevalence at fine spatial resolution, calling for the need to maintain some form of reduced-scale national prevalence surveys in non-epidemic periods. The model framework is disease-agnostic and could therefore be adapted to different diseases and incorporated into a multiplex surveillance system for early detection of emerging local outbreaks.

Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models

The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown. In this review, our main focus was on finding mathematical models which take into the account both the time-varying and spatial nature of wastewater-based metrics into account. We used six main characteristics as our assessment criteria: i) modelling approach; ii) temporal coverage; iii) spatial coverage; iv) sample size; v) wastewater sampling method; and vi) covariates included in the modelling. The majority of studies in the early phases of the pandemic recognized the temporal association of SARS-CoV-2 RNA concentration level in wastewater with the number of COVID-19 cases, ignoring their spatial context. We examined 15 studies up to April 2023, focusing on models considering both temporal and spatial aspects of wastewater metrics. Most early studies correlated temporal SARS-CoV-2 RNA levels with COVID-19 cases but overlooked spatial factors. Linear regression and SEIR models were commonly used (n = 10, 66.6 % of studies), along with machine learning (n = 1, 6.6 %) and Bayesian approaches (n = 1, 6.6 %) in some cases. Three studies employed spatio-temporal modelling approach (n = 3, 20.0 %). We conclude that the development, validation and calibration of further spatio-temporally explicit models should be done in parallel with the advancement of wastewater metrics before the potential of wastewater as a surveillance tool can be fully realised.