Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis

Proverbio, Daniele; Kemp, Françoise; Magni, Stefano; Ogorzaly, Leslie; Cauchie, Henry‐Michel; Skupin, Alexander; Aalto, Atte

doi:10.1016/j.scitotenv.2022.154235

Cited by 37 publications

(32 citation statements)

References 53 publications

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“…WWS has been used for identifying increasing trends of community-level infections and predicting epidemic peaks with a reasonable anticipation time, thus providing opportune public health interventions [17][18][19][20][21]. Furthermore, by the introduction of genome sequencing methodologies, WWS has expanded from detecting traces of viral RNA by RT-qPCR to tracking the introduction and prevalence of mutations associated with VOCs circulating in the community [22].…”

Section: Introductionmentioning

confidence: 99%

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

et al. 2023

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SARS-CoV-2 surveillance of viral populations in wastewater samples is recognized as a useful tool for monitoring epidemic waves and boosting health preparedness. Next generation sequencing of viral RNA isolated from wastewater is a convenient and cost-effective strategy to understand the molecular epidemiology of SARS-CoV-2 and provide insights on the population dynamics of viral variants at the community level. However, in low- and middle-income countries, isolated groups have performed wastewater monitoring and data has not been extensively shared in the scientific community. Here we report the results of monitoring the co-circulation and abundance of variants of concern (VOCs) of SARS-CoV-2 in Uruguay, a small country in Latin America, between November 2020—July 2021 using wastewater surveillance. RNA isolated from wastewater was characterized by targeted sequencing of the Receptor Binding Domain region within the spike gene. Two computational approaches were used to track the viral variants. The results of the wastewater analysis showed the transition in the overall predominance of viral variants in wastewater from No-VOCs to successive VOCs, in agreement with clinical surveillance from sequencing of nasal swabs. The mutations K417T, E484K and N501Y, that characterize the Gamma VOC, were detected as early as December 2020, several weeks before the first clinical case was reported. Interestingly, a non-synonymous mutation described in the Delta VOC, L452R, was detected at a very low frequency since April 2021 when using a recently described sequence analysis tool (SAM Refiner). Wastewater NGS-based surveillance of SARS-CoV-2 is a reliable and complementary tool for monitoring the introduction and prevalence of VOCs at a community level allowing early public health decisions. This approach allows the tracking of symptomatic and asymptomatic individuals, who are generally under-reported in countries with limited clinical testing capacity. Our results suggests that wastewater-based epidemiology can contribute to improving public health responses in low- and middle-income countries.

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Section: Introductionmentioning

confidence: 99%

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

et al. 2023

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“…Early efforts during the COVID-19 pandemic relied on relatively simple correlation analyses between SARS-CoV-2 RNA concentrations and COVID-19 cases or hospitalizations in a community. As research efforts continue to develop numerical techniques for surveillance of SARS-CoV-2 and other targets, 77 , 78 attention to predictive modeling techniques and integration of wastewater data into other epidemiological data analyses will remain critical. Further, retrospective analyses of the volumes of data that have been collected during the COVID-19 pandemic may reveal important insights that will inform our response to future pandemics.…”

Section: Discussionmentioning

confidence: 99%

Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs

Hoar

McClary-Gutierrez

Wolfe

et al. 2022

Environ Health Perspect

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Background: In just over 2 years, tracking the COVID-19 pandemic through wastewater surveillance advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. Objectives: We examined the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition from early monitoring efforts to more formalized programs within the public health system. Discussion: Although wastewater surveillance has rapidly developed as a useful public health tool for tracking COVID-19, there remain technical challenges and open scientific questions that academic researchers are equipped to address. This includes validating methodology and backfilling important knowledge gaps, such as fate and transport of surveillance targets and epidemiological links to wastewater concentrations. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and draw useful lessons on how to promote synergy between different areas of expertise. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should promote knowledge co-development. We believe active involvement of academic researchers will contribute to building robust surveillance programs that will ultimately provide new insights into population health. https://doi.org/10.1289/EHP11519

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“…To forecast the unknowable epidemic data, [34] created a wastewater-based compartmental epidemic model with two-phase vaccination dynamics and immune evasion. A stochastic SEIR model was applied to bridge the gap between the number of infected cases and viral concentration in wastewater [35]. The authors of [36] developed a stochastic SIR model and solved it using the Monte Carlo method to forecast the behavior of the pandemic including viral load data and a variable infection rate to account for the effect of mitigation measures.…”

Section: Methodsmentioning

confidence: 99%

Simulation of COVID-19 Epidemic from Potential Viral Loads in Saudi Arabian Wastewater Treatment Plants

Meetei,

Msmali,

Ahmadini

et al. 2023

Preprint

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SARS-CoV-2 is a contagious respiratory virus that has been discovered in sewage, human waste, and wastewater treatment facilities. Wastewater surveillance has been considered one of the lowest-cost means of testing for tracking the COVID-19 outbreak in communities. This paper highlights the dynamics of the virus’s infection, persistence, and occurrence in wastewater treatment plants. Our aim is to develop and implement a mathematical model to infer the epidemic dynamics from the possible density of SARS-CoV-2 viral load in wastewater. We present a log-normal model and fractional order of susceptible-exposed-infected-recovery (SEIR) epidemic model for predicting the spread of the COVID-19 disease from the wastewater data. We study the dynamic properties of the fractional order SEIR model with respect to the fractional ordered values. The model is used to comprehend how the coronavirus spreads through wastewater treatment plants in Saudi Arabia. Our modeling approach can help with wastewater surveillance for early prediction and cost-effective monitoring of the epidemic outbreak in a situation of low testing capacity.

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Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis

Cited by 37 publications

References 53 publications

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing

Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs

Simulation of COVID-19 Epidemic from Potential Viral Loads in Saudi Arabian Wastewater Treatment Plants

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