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>

Temporal assessment of SARS-CoV-2 detection in wastewater and its epidemiological implications in COVID-19 case dynamics DOI Creative Commons
Lin Li, Laura Haak, Madeline Carine

et al.

Heliyon, Journal Year: 2024, Volume and Issue: 10(8), P. e29462 - e29462

Published: April 1, 2024

This research evaluated the relationship between daily new Coronavirus Disease 2019 (COVID-19) cases and Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) concentrations in wastewater, followed by effects of differential SARS-CoV-2 shedding loads across various COVID-19 outbreaks. Linear regression analyses were utilized to examine lead time signal wastewater relative clinical cases. During Delta wave, no was evident, highlighting limited predictive capability monitoring during this phase. However, significant times observed Omicron potentially attributed testing capacity overload subsequent case reporting delays or changes patterns. Post-Omicron wave (Febuary 23 May 19, 2022), discernible, whereas following lifting state emergency (May 30, 2022 2023), correlation coefficient increased demonstrated potential surveillance as an early warning system. Subsequently, we explored virus through feces, operationalized ratio varied significantly Delta, Omicron, other variants post-state-emergency phases, with Kruskal-Wallis H test confirming a difference medians these stages (P < 0.0001). Despite its promise, disease prevalence presents several challenges, including variability, data interpretation complexity, impact environmental factors on viral degradation, lack standardized procedures. Overall, our findings offer insights into concentrations, variation different pandemic underscore promise limitations system for trends.

Language: Английский

Citations

4
SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic DOI Creative Commons
Patrick M. D’Aoust, Nada Hegazy,

Nathan T. Ramsay

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: June 21, 2024

Abstract During the COVID-19 pandemic, Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by early work and successful forecasts waves in city Ottawa, Ontario. This manuscript presents dataset from January 1, 2021, March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes PMMoV 107 sites across all 34 public health units covering 72% province’s 26.2% Canada’s population. Sampling occurred 2–7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, flowrates. In doing so, this ensures data availability metadata preservation support future research epidemic preparedness through detailed analyses modeling. The has been crucial tracking disease locally, especially rise Omicron variant decline clinical testing, highlighting wastewater-based surveillance’s role estimating incidence

Language: Английский

Citations

4
Wastewater solids drive comparability of sampling methods for SARS-CoV-2 wastewater and environmental surveillance DOI Creative Commons

Md Pervez Kabir,

Elizabeth Renouf,

Lakshmi Pisharody

et al.

Journal of environmental chemical engineering, Journal Year: 2025, Volume and Issue: unknown, P. 115374 - 115374

Published: Jan. 1, 2025

Language: Английский

Citations

0
Variability of Clinical Metrics in Small Population Communities Drive Perceived Wastewater and Environmental Surveillance Data Quality: Ontario, Canada-Wide Study DOI Creative Commons
Nada Hegazy, Katy Peng, Patrick M. D’Aoust

et al.

ACS ES&T Water, Journal Year: 2025, Volume and Issue: 5(4), P. 1605 - 1619

Published: March 7, 2025

The emergence of COVID-19 in Canada has led to over 4.9 million cases and 59,000 deaths by May 2024. Traditional clinical surveillance metrics (hospital admissions laboratory-positive cases) were complemented with wastewater environmental monitoring (WEM) monitor SARS-CoV-2 incidence. However, challenges public health integration WEM persist due perceived limitations data quality, potentially driving inconsistent correlations variability lead times. This study investigates how factors like population size, measurement magnitude, site isolation status, hospital admissions, affect Ontario. analysis uncovers a direct relationship between the size surveyed sewersheds, while magnitude was not directly impacted size. Higher observed smaller likely reducing correlation strength for inferring Population significantly influenced thresholds identified at ∼66,000 inhabitants strong WEM-hospital ∼68,000 WEM-laboratory-positive during waned vaccination periods Ontario (the Omicron BA.1 wave). During significant immunization BA.2 wave), these increased ∼187,000 238,000, respectively. These findings highlight benefit strategic interventions, especially communities. provides insights enhancing decision making disease through WEM, applicable other diseases.

Language: Английский

Citations

0
Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19 DOI Creative Commons
Ryland Corchis-Scott, Qiudi Geng,

Abdul Monem Al Riahi

et al.

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

Published: May 17, 2023

Wastewater surveillance has gained traction during the COVID-19 pandemic as an effective and non-biased means to track community infection. While most relies on samples collected at municipal wastewater treatment plants, is more actionable when are “upstream” where mitigation of transmission tractable. This report describes results for SARS-CoV-2 residence halls a university campus aimed preventing outbreak escalation by mitigating spread. Another goal was estimate fecal shedding rates in non-clinical setting. Passive sampling devices were deployed sewer laterals originating from frequency twice weekly fall 2021 Delta variant concern continued circulate across North America. A positive detection part routine late November triggered daily monitoring further isolated signal single wing one hall. Detection within over period 3 consecutive days led coordinated rapid antigen testing campaign targeting hall occupants identification isolation infected individuals. With knowledge number individuals COVID-19, estimated range 3.70 log10 gc ‧ g feces −1 5.94 . These reinforce efficacy early indicator infection congregate living settings. Detections can trigger public health measures ranging enhanced communications targeted quarantine.

Language: Английский

Citations

8
An exploration of the relationship between wastewater viral signals and COVID-19 hospitalizations in Ottawa, Canada DOI Creative Commons
Katy Peng,

Elizabeth Renouf,

C. B. Dean

et al.

Infectious Disease Modelling, Journal Year: 2023, Volume and Issue: 8(3), P. 617 - 631

Published: June 7, 2023

Monitoring of viral signal in wastewater is considered a useful tool for monitoring the burden COVID-19, especially during times limited availability testing. Studies have shown that COVID-19 hospitalizations are highly correlated with signals and increases can provide an early warning increasing hospital admissions. The association likely nonlinear time-varying. This project employs distributed lag model (DLNM) (Gasparrini et al., 2010) to study exposure-response delayed SARS-CoV-2 using relevant data from Ottawa, Canada. We consider up 15-day time average SARS-CoV N1 N2 gene concentrations hospitalizations. expected reduction hospitalization adjusted vaccination efforts. A correlation analysis verifies time-varying relationship. Our DLNM based yields reasonable estimate enhances our understanding signals.

Language: Английский

Citations

8
Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region DOI Creative Commons
Jianxian Sun, Minqing Ivy Yang, Jiaxi Peng

et al.

Water Research X, Journal Year: 2024, Volume and Issue: 22, P. 100221 - 100221

Published: Jan. 1, 2024

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between biomarkers noticed by independent studies these methods since late 2021. reason is presumed be due mutations targeted N1 probe. In this study, we systematically investigated unequivocally confirmed that underlying for was probe target, single mutation could cause significant drop signal. We first proportion related wastewater samples (Jan 2021-Dec 2022) nested PCR LC-MS. Based on relative proportions alleles, separated data into four time periods corresponding different variant waves: Period I (Alpha Delta waves with 0 mutation), II (BA.1/BA.2 found all Omicron strains), III (BA.5.2* wave mutations), IV (BQ.1* mutations). Significantly lower copies N2 from Periods II-IV compared those observed wastewater. To further pinpoint extent which each impacted quantification, response among synthetic oligomers mutations. This study highlighted impact even just one or qPCR-based SARS-CoV-2.

Language: Английский

Citations

2
A Potent Recombinant Polyclonal Antibody Therapeutic for Protection Against New Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern DOI Creative Commons
Nicholas Wayham,

Ariel R. Niedecken,

Jan Fredrik Simons

et al.

The Journal of Infectious Diseases, Journal Year: 2023, Volume and Issue: 228(5), P. 555 - 563

Published: April 17, 2023

Abstract Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) possess mutations that prevent antibody therapeutics from maintaining antiviral binding and neutralizing efficacy. Monoclonal antibodies (mAbs) shown to neutralize Wuhan-Hu-1 SARS-CoV-2 (ancestral) strain have reduced potency against newer variants. Plasma-derived polyclonal hyperimmune drugs improved neutralization breadth compared with mAbs, but lower titers require higher dosages for treatment. We previously developed a highly diverse, recombinant therapeutic anti-SARS-CoV-2 immunoglobulin (rCIG). rCIG was plasma-derived or mAb standards showed across World Health Organization variants; however, its some relative ancestral, particularly omicron. Omicron-specific sequences were enriched yeast expressing rCIG-scFv exhibited increased omicron BA.2 while ancestral neutralization. Polyclonal libraries such as can be utilized develop present future threats.

Language: Английский

Citations

6
Bayesian sequential approach to monitor COVID-19 variants through test positivity rate from wastewater DOI Creative Commons
J. Cricelio Montesinos-López, Maria L. Daza–Torres, Yury E. García

et al.

mSystems, Journal Year: 2023, Volume and Issue: unknown

Published: July 25, 2023

ABSTRACT Deployment of clinical testing on a massive scale was an essential control measure for curtailing the burden severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and magnitude COVID-19 (coronavirus disease 2019) pandemic during its waves. As progressed, new preventive surveillance mechanisms emerged. Implementation vaccine programs, wastewater (WW) surveillance, at-home antigen tests reduced demand mass SARS-CoV-2 testing. Unfortunately, reductions in test reporting rates also availability public health data to support decision-making. This paper proposes sequential Bayesian approach estimate positivity rate (TPR) using RNA concentrations measured WW through adaptive scheme incorporating changes virus dynamics. The proposed modeling framework applied from two treatment plants California; City Davis University California, campus. TPR estimates are used compute thresholds Centers Disease Control Prevention low (<5% TPR), moderate (5%–8% substantial (8%–10% high (>10% TPR) transmission. effective reproductive number calculated data. provides insights into dynamics evolution analytical that combines different sources continue monitoring trends. These results can provide guidance reduce future outbreaks as variants emerge. IMPORTANCE We propose statistical model correlate with monitor trends help overcome limitations relying only case detection. pose nonautonomous nature prolonged pandemic. is modeled beta regression covariable. resulting allows us based measurements incorporates viral transmission scheme.

Language: Английский

Citations

6
Correlation between wastewater and COVID-19 case incidence rates in major California sewersheds across three variant periods DOI Creative Commons
Angela Rabe,

Sindhu Ravuri,

Elisabeth Burnor

et al.

Journal of Water and Health, Journal Year: 2023, Volume and Issue: 21(9), P. 1303 - 1317

Published: Sept. 1, 2023

Monitoring for COVID-19 through wastewater has been used adjunctive public health surveillance, with SARS-CoV-2 viral concentrations in correlating incident cases the same sewershed. However, generalizability of these findings across sewersheds, laboratory methods, and time periods changing variants underlying population immunity not well described. The California Department Public Health partnered six treatment plants starting January 2021 to monitor SARS-CoV-2, analyses performed at four laboratories. Using reported PCR-confirmed within each sewershed, relationship between case incidence rates collected over 14 months was evaluated using Spearman's correlation linear regression. Strong correlations were observed when averaged (10- 7-day moving window cases, respectively, ρ = 0.73-0.98 N1 gene target). Correlations remained strong three distinct circulating vaccination (winter 2020-2021/Alpha, summer 2021/Delta, winter 2021-2022/Omicron). Linear regression revealed that slopes associations varied by dominant variant concern, (β 0.45-1.94). These support surveillance as an tool community trends.

Language: Английский

Citations

6