Robust smoothing of left-censored time series data with a dynamic linear model to infer SARS-CoV-2 RNA concentrations in wastewater DOI Creative Commons
Luke Lewis-Borrell, J. C. E. Irving,

Chris J. Lilley

et al.

AIMS Mathematics, Journal Year: 2023, Volume and Issue: 8(7), P. 16790 - 16824

Published: Jan. 1, 2023

<abstract><p>Wastewater sampling for the detection and monitoring of SARS-CoV-2 has been developed applied at an unprecedented pace, however uncertainty remains when interpreting measured viral RNA signals their spatiotemporal variation. The proliferation measurements that are below a quantifiable threshold, usually during non-endemic periods, poses further challenge to interpretation time-series analysis data. Inspired by research in use custom Kalman smoother model estimate true level concentrations wastewater, we propose alternative left-censored dynamic linear model. Cross-validation both models alongside simple moving average, using data from 286 sewage treatment works across England, allows comprehensive validation proposed approach. presented is more parsimonious, faster computational time represented flexible modelling framework than equivalent smoother. Furthermore show how wastewater data, transformed such models, correlates closely with regional case rate positivity as published Office National Statistics (ONS) Coronavirus (COVID-19) Infection Survey. modelled output robust therefore capable better complementing traditional surveillance untransformed or providing additional confidence utility public health decision making.</p> <p>La détection et la du dans les eaux usées ont été développées réalisées à un rythme sans précédent, mais l'interprétation des mesures de en ARN viral, leurs variations spatio-temporelles, pose question. En particulier, l'importante proportion deçà seuil quantification, généralement pendant périodes non endémiques, constitue défi pour l'analyse ces séries temporelles. Inspirés par travail recherche ayant produit lisseur adapté estimer réelles partir ce type données, nous proposons nouveau modèle linéaire dynamique avec censure gauche. Une croisée lisseurs, ainsi que d'un lissage moyenne glissante, sur données provenant stations d'épuration couvrant l'Angleterre, valide façon complète l'approche proposée. Le présenté est plus parcimonieux, offre cadre modélisation nécessite temps calcul réduit rapport au Lisseur équivalent. Les issues lissées sont outre fortement corrélées le taux d'incidence régional bureau statistiques nationales Elles se montrent robustes brutes, ou donc même compléter traditionnelle, renforçant confiance l'épidémiologie fondée son utilité prise décisions santé publique.</p></abstract>

Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond DOI
Michael D. Parkins,

Bonita E. Lee,

Nicole Acosta

et al.

Clinical Microbiology Reviews, Journal Year: 2023, Volume and Issue: 37(1)

Published: Dec. 14, 2023

SUMMARY Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of coronavirus disease 2019 (COVID-19) pandemic. The power and potential this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical within monitored populations but also, fact, functioned as a leading indicator. Teams from across globe innovated novel approaches by which wastewater could be collected diverse sewersheds ranging treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods high-risk buildings such long-term care facilities (LTCF). Efficient processes enabled extraction concentration highly dilute matrix. Molecular genomic tools identify, quantify, characterize its various variants adapted programs applied these mixed environmental systems. Novel data-sharing allowed information mobilized made immediately available public health government decision-makers even public, enabling evidence-informed decision-making based on local dynamics. WBS since been recognized tool transformative potential, providing near-real-time cost-effective, objective, comprehensive, inclusive data changing prevalence measured analytes space time populations. However, consequence rapid innovation hundreds teams simultaneously, tremendous heterogeneity currently exists literature. This manuscript provides state-of-the-art review established details current work underway expanding scope other infectious targets.

Language: Английский

Citations

52
Understanding the dynamic relation between wastewater SARS-CoV-2 signal and clinical metrics throughout the pandemic DOI
Nada Hegazy,

Aaron Cowan,

Patrick M. D’Aoust

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 853, P. 158458 - 158458

Published: Sept. 6, 2022

Language: Английский

Citations

42
Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019–December, 2021) DOI Creative Commons
Elizabeth T. Rogawski McQuade, Isobel M. Blake, Stephanie A. Brennhofer

et al.

The Lancet Microbe, Journal Year: 2023, Volume and Issue: 4(6), P. e442 - e451

Published: April 3, 2023

Language: Английский

Citations

23
Simple methods for early warnings of COVID-19 surges: Lessons learned from 21 months of wastewater and clinical data collection in Detroit, Michigan, United States DOI Open Access
Liang Zhao,

Yangyang Zou,

Randy E. David

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 864, P. 161152 - 161152

Published: Dec. 23, 2022

Language: Английский

Citations

29
Assessment of seasonality and normalization techniques for wastewater-based surveillance in Ontario, Canada DOI Creative Commons
Hadi A. Dhiyebi, Joud Abu Farah, Heather Ikert

et al.

Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11

Published: Aug. 30, 2023

Introduction Wastewater-based surveillance is at the forefront of monitoring for community prevalence COVID-19, however, continued uncertainty exists regarding use fecal indicators normalization SARS-CoV-2 virus in wastewater. Using three communities Ontario, sampled from 2021–2023, seasonality a viral indicator (pepper mild mottle virus, PMMoV) and utility data to improve correlations with clinical cases was examined. Methods Wastewater samples Warden, Humber Air Management Facility (AMF), Kitchener were analyzed SARS-CoV-2, PMMoV, crAssphage. The PMMoV flow rates examined compared by Season-Trend-Loess decomposition analysis. effects using crAssphage, comparing episode date (CBED) during 2021. Results Seasonal analysis demonstrated that had similar trends AMF peaks January April 2022 low concentrations (troughs) summer months. Warden but more sporadic between troughs concentrations. Flow not correlated very weak ( r = 0.12). Despite differences among sewersheds, unnormalized (raw N1–N2) concentration wastewater n 99–191) strongly CBED 0.620–0.854) Additionally, did significantly reduced Kitchener. crAssphage 29–57) all sites different raw N1–N2 CBED. Discussion Differences seasonal biomarkers caused sewershed characteristics (flow, input, etc.) may play role determining how effective be improving (or not). This study highlights importance assessing influence on normalized or other viruses concern. Fecal used normalize target interest help hinder establishing outcomes wastewater-based needs considered carefully across seasons sites.

Language: Английский

Citations

18
Wastewater Surveillance Provides Spatiotemporal SARS-CoV-2 Infection Dynamics DOI Creative Commons

Xiawan Zheng,

Kathy Leung, Xiaoqing Xu

et al.

Engineering, Journal Year: 2024, Volume and Issue: 40, P. 70 - 77

Published: March 15, 2024

Wastewater surveillance can leverage its wide coverage, population-based sampling, and high monitoring frequency to capture citywide pandemic trends independent of clinical surveillance. Here we conducted a 9-month daily wastewater for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 12 treatment plants (WWTPs), covering approximately 80% the population, monitor infection dynamics in Hong Kong. We found that SARS-CoV-2 virus concentration was correlated with number reported cases reached two peaks three days earlier during study period. In addition, different methods were established estimate prevalence/incidence rates measurements. The estimated results consistent findings programmes (rapid antigen test (RAT) serology surveillance), but higher than by Centre Health Protection (CHP) Moreover, effective reproductive (Rt) measurements reflect both regional transmission dynamics. Our demonstrate large-scale intensive WWTPs provides cost-effective timely public health information, especially when is inadequate costly. This approach also insights into at spatiotemporal resolutions, facilitating formulation control policies targeted resource allocation.

Language: Английский

Citations

6
Omicron COVID-19 Case Estimates Based on Previous SARS-CoV-2 Wastewater Load, Regional Municipality of Peel, Ontario, Canada DOI Creative Commons
Lydia Cheng, Hadi A. Dhiyebi,

Monali Varia

et al.

Emerging infectious diseases, Journal Year: 2023, Volume and Issue: 29(8)

Published: July 13, 2023

We determined correlations between SARS-CoV-2 load in untreated water and COVID-19 cases patient hospitalizations before the Omicron variant (September 2020-November 2021) at 2 wastewater treatment plants Regional Municipality of Peel, Ontario, Canada. Using pre-Omicron correlations, we estimated incident during outbreaks (November 2021-June 2022). The strongest correlation occurred 1 day after sampling (r = 0.911). 4 days 0.819). At peak BA.2 outbreak April 2022, reported were underestimated 19-fold because changes clinical testing. Wastewater data provided information for local decision-making are a useful component surveillance systems.

Language: Английский

Citations

13
Expansion of wastewater-based disease surveillance to improve health equity in California’s Central Valley: sequential shifts in case-to-wastewater and hospitalization-to-wastewater ratios DOI Creative Commons
Krystin F. Kadonsky, Colleen C. Naughton,

Mirjana Susa

et al.

Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11

Published: June 30, 2023

Over a third of the communities (39%) in Central Valley California, richly diverse and important agricultural region, are classified as disadvantaged-with inadequate access to healthcare, lower socio-economic status, higher exposure air water pollution. The majority racial ethnic minorities also at risk COVID-19 infection, hospitalization, death according Centers for Disease Control Prevention. Healthy Together established wastewater-based disease surveillance (WDS) program that aims achieve greater health equity region through partnership with Sewer Coronavirus Alert Network. WDS offers cost-effective strategy monitor trends SARS-CoV-2 community infection rates.

Language: Английский

Citations

13
Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data DOI Creative Commons
David Champredon, Devan Becker, Shelley Peterson

et al.

BMC Infectious Diseases, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 29, 2024

Abstract Background The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition numerous SARS-CoV-2lineages have observed in near real-time. Lineage identification, traditionally from clinical samples, can also be determined by sampling wastewater sewersheds serving populations interest. Variants concern (VOCs) lineages associated with increased transmissibility and/or severity are particular Method Here, we consider data sources to assess VOCs Canada retrospectively. Results We show that, overall, wastewater-based VOC identification provides similar insights surveillance based samples. Based data, synchrony introduction as well speeds across most Canadian provinces despite geographical size country differences provincial public health measures. Conclusion particular, it took approximately four months for Alpha Delta contribute half incidence. contrast, Omicron achieved same contribution less than one month. This study significant benchmarks enhance planning future VOCs, some extent pandemics caused other pathogens, quantifying rate invasion Canada.

Language: Английский

Citations

5
Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era DOI Creative Commons
Federica Armas, Franciscus Chandra, Wei Lin Lee

et al.

Environment International, Journal Year: 2022, Volume and Issue: 171, P. 107718 - 107718

Published: Dec. 23, 2022

SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of population's infections. In the past two years, WBS has proven to be crucial managing pandemic across different geographical regions. However, changing context due high levels COVID-19 vaccination warrants closer examination its implication towards WBS. Two main questions were raised: 1) Does cause shedding viral signatures without infection? 2) affect relationship between wastewater and clinical data? To answer, we review historical reports from vaccines in use prior including polio, rotavirus, influenza measles infection provide perspective on implications strategies with regard potential into sewershed. Additionally, reviewed studies that looked data how campaigns could have affected relationship. Finally, analyzing Netherlands, observed changes concomitant increasing coverage switches dominant variants concern. First, no vaccine-derived is expected current commercial pipeline may confound interpretation data. Secondly, breakthrough infections vaccinated individuals contribute significantly signals must interpreted light dynamics new

Language: Английский

Citations

21