Bayesian sequential approach to monitor COVID-19 variants through positivity rate from wastewater

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 11, 2023

Trends in COVID-19 infection have changed throughout the pandemic due to myriad factors, including changes transmission driven by social behavior, vaccine development and uptake, mutations virus genome, public health policies. Mass testing was an essential control measure for curtailing burden of monitoring magnitude during its multiple phases. However, as progressed, new preventive surveillance mechanisms emerged. Implementing programs, wastewater (WW) surveillance, at-home tests reduced demand mass severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. This paper proposes a sequential Bayesian approach estimate positivity rate (PR) using SARS-CoV-2 RNA concentrations measured WW through adaptive scheme incorporating dynamics. PR estimates are used compute thresholds data CDC low, substantial, high transmission. The effective reproductive number calculated from data. provides insights into dynamics evolution analytical framework that combines different sources continue trends. These results can provide guidance reduce future outbreaks variants emerge. proposed modeling applied City Davis campus University California Davis.

Language: Английский

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Leveraging wastewater surveillance to actively monitor Covid‐19 community dynamics in rural areas with reduced reliance on clinical testing

Applied Research, Journal Year: 2024, Volume and Issue: 3(5)

Published: March 5, 2024

Abstract The prevalence of coronavirus disease 2019 (Covid‐19) in the community has become more difficult to gauge utilizing clinical testing due a decrease reported test results stemming from availability at‐home kits and reduction number cases seeking medical treatment. purpose this study was examine trend diminishing correlation between Covid‐19 wastewater‐based surveillance epidemiological data as home became available Eastern Upper Peninsula Michigan. Wastewater grab samples were collected weekly 16 regional locations June 2021 December 2022. Samples analyzed for severe acute respiratory syndrome 2 (SARS‐CoV‐2) N1 N2 viral particles using reverse transcriptase digital droplet polymerase chain reaction (RT ddPCR). gene copies correlated with cases. t used determine deterioration point. Clinical postdeterioration calculated high‐correlated predeterioration linear regression. Correlation SARS‐CoV‐2 deteriorated after February 1, This corresponds timeframe which commercially United States. increase likely contributed positive tests early 2022, providing an unrealistic picture presence community. As measures reduce exposure such personal masking, testing, social isolating, quarantining continue decline, wastewater may be best method public health professionals remain aware virus dynamics localized regions. Time‐series modeling adds another layer information when is unobtainable or underreported.

Language: Английский

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Sewer Transport Conditions and Their Role in the Decay of Endogenous SARS-CoV-2 and Pepper Mild Mottle Virus from Source to Collection

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 2, 2024

Abstract This study presents a comprehensive analysis of the decay patterns endogenous SARS-CoV-2 and Pepper mild mottle virus (PMMoV) within wastewaters spiked with stool from infected patients expressing COVID-19 symptoms, hence explores PMMoV targets in source to collection sample. Stool samples were used as viral material more accurately mirror real-world processes compared traditionally lab-propagated spike-ins. As such, this includes data on early stages that are typically overlooked when performing studies harvested wastewater treatment plants contain already-degraded material. The two distinct sewer transport conditions dynamic suspended bed near-bed simulated at temperatures 4°C, 12°C 20°C elucidate under these dominant infrastructure. was over 35 hours, representing typical flow conditions, whereas extended 60 days reflect prolonged settling solids systems during reduced periods. In transport, no observed for SARS-CoV-2, PMMoV, or total RNA 35-hour period, temperature ranging 4°C had noticeable effect. Conversely, experiments simulating revealed significant decreases concentrations by day 2, 3. Only exhibited clear trend increasing constant higher temperatures, suggesting while influences dynamics, its impact may be less than previously assumed, particularly is bound dissolved organic matter wastewater. First order models inadequate fitting curves conditions. F-tests confirmed superior fit two-phase model first across 20°C. Finally, most importantly, normalization emerged an appropriate approach correcting time exposed These findings highlight importance considering point entry sewers, strategies assessing modelling rates systems. also emphasizes need ongoing research into diverse multifaceted factors influence rates, which crucial accurate public health monitoring response strategies.

Language: Английский

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The first detection of SARS-CoV-2 RNA in the wastewater of Bucharest, Romania

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 17, 2024

Wastewater-based epidemiology (WBE) has been previously used as a tool for pathogen identification within communities. After the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) outbreak, in 2020, Daughton proposed implementation of wastewater surveillance strategy that could determine incidence COVID-19 (coronavirus disease 2019) nationally. Individuals various stages infection, including presymptomatic, asymptomatic and symptomatic patients, can be identified carriers virus their urine, saliva, stool other bodily secretions. Studies using this method were conducted to monitor prevalence high-density populations, such cities but also smaller communities, schools college campuses. The aim pilot study was assess feasibility effectiveness Bucharest, Romania, samples collected weekly from seven locations between July September 2023. RNA (ribonucleic acid) extraction, followed by dPCR (digital polymerase chain reaction) analysis, performed detect viral genetic material. Additionally, NGS (next generation sequencing) technology identify circulating variants Romania. Preliminary results indicate successful detection wastewater, providing valuable insights into circulation community.

Language: Английский

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Robust smoothing of left-censored time series data with a dynamic linear model to infer SARS-CoV-2 RNA concentrations in wastewater

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>

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