A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities

Nourbakhsh, Shokoofeh; Fazil, Aamir; Mangat, Chand S.; Peterson, Shelley; Daigle, Jade; Langner, Stacie; Shurgold, Jayson; D’Aoust, Patrick M.; Delatolla, Robert; Mercier, Élisabeth; Pang, Xiaoli; Lee, Bonita E.; Stuart, Rebecca; Wijayasri, Shinthuja; Champredon, David

doi:10.1016/j.epidem.2022.100560

Cited by 78 publications

(74 citation statements)

References 93 publications

(95 reference statements)

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“…Our statistical modelling has provided a description of trends in virus loads at a local level by properly weighing all available wastewater measurements. In contrast, other modelling studies have focused on relating national or subnational virus loads to case notification data or hospitalisations using mechanistic modelling, with the aim to estimate the indicidence and prevalence of the number of infections over time ( [24,25] and references therein). The two approaches serve different purposes, and each has its strengths and limitations.…”

Section: Discussionmentioning

confidence: 99%

Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program

Boven

Hetebrij

Swart

et al. 2022

Preprint

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SUMMARY Background Surveillance of SARS-CoV-2 in wastewater offers an unbiased and near real-time tool to track circulation of SARS-CoV-2 at a local scale, next to other epidemic indicators such as hospital admissions and test data. However, individual measurements of SARS-CoV-2 in sewage are noisy, inherently variable, and can be left-censored. Aim We aimed to infer latent virus loads in a comprehensive sewage surveillance program that includes all sewage treatment plants (STPs) in the Netherlands and covers 99.6% of the Dutch population. Methods A multilevel Bayesian penalized spline model was developed and applied to estimate time- and STP-specific virus loads based on water flow adjusted SARS-CoV-2 qRT-PCR data from 1-4 sewage samples per week for each of the >300 STPs. Results The model provided an adequate fit to the data and captured the epidemic upsurges and downturns in the Netherlands, despite substantial day-to-day measurement variation. Estimated STP virus loads varied by more than two orders of magnitude, from approximately 1012 (virus particles per 100,000 persons per day) in the epidemic trough in August 2020 to almost 1015 in many STPs in January 2022. Epidemics at the local levels were slightly shifted between STPs and municipalities, which resulted in less pronounced peaks and troughs at the national level. Conclusion Although substantial day-to-day variation is observed in virus load measurements, wastewater-based surveillance of SARS-CoV-2 can track long-term epidemic progression at a local scale in near real-time, especially at high sampling frequency.

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Section: Discussionmentioning

confidence: 99%

Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program

Boven

Hetebrij

Swart

et al. 2022

Preprint

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“…This is similar to the geographical trends in wastewater results for these sewerzones, which are also variable. 22 Although other research purports a transfer function relating wastewater measures and clinical prevalence is possible, 15,16,18 it has not been quantified before. Xiao et al 17 suggests a ratio of wastewater viral copy numbers to reported COVID-19 cases (WC ratio) which changes over time, whereas our model adapts over time but with a consistent transfer function.…”

Section: Discussionmentioning

confidence: 99%

“…6 The use of systematic serological surveys for calibrating wastewater measurements removes much of the selection bias observed in previous relationships. [13][14][15][16][17] Although seropositivity provides estimates of past infection, an increase in seropositivity over a defined period is likely to be a reliable indicator of the spread of infection. Hence, over the course of the eight-month project, enriched contextual data were provided to city decision makers and stakeholders to inform long-term trends in infection rates as well as the levels of SARS-CoV-2 in local wastewater.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Previous combined wastewater and serological surveys at a community scale have focused on Hepatitis A and E viruses. 11,12 Existing SARS-CoV-2 wastewater to community COVID-19 case models have been fit around results obtained from convenience sampling, models which may underrepresent community trends, [13][14][15][16][17] as well as limited random samples of communities via SARS-CoV-2 in nasal swabs 10 or blood bank serological surveys. 15,18 Nonetheless, robust longitudinal estimates of community serology are more appropriate to interpret wastewater measurements.…”

Section: Introductionmentioning

confidence: 99%

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Quantifying the relationship between sub-population wastewater samples and community-wide SARS-CoV-2 seroprevalence

Smith

Holm

Keith

et al. 2022

Preprint

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BackgroundWastewater-based epidemiology is a promising approach but robust epidemiological models to relate wastewater to community prevalence are lacking. Assessments of SARS-CoV-2 infection rates have relied primarily on convenience sampling, which does not provide reliable estimates of community prevalence because of inherent biases.MethodsFrom August 2020 to February 2021, we conducted a serial stratified randomized samplings to estimate the prevalence of anti-SARS-CoV-2 antibodies in 3,717 participants, and weekly sampling of community wastewater for SARS-CoV-2 concentrations in Jefferson County, KY. With the use of a Susceptible, Infected, Recovered (SIR)-type model, we obtained longitudinal estimates of prevalence and compared these with wastewater concentration, using regression analysis.FindingsModel analysis revealed significant temporal differences in epidemic peaks; the average incidence rate based on serological sampling in some areas was up to 50% higher than health department rates based on convenience sampling. The model-estimated average prevalence rates correlated well with wastewater (correlation=0·63). In regression analysis, a weekly unit increase in wastewater concentration of SARS-CoV-2 corresponded to an average increase of between 1-1·3 cases of SARS-CoV-2 infection per 100K residents.InterpretationPublicly available health department incidence rates vastly underestimate true community incidence and wastewater has a high potential to provide robust estimates of community spread of infection.Research in contextEvidence before this studyAdministratively reported clinical case rates of coronavirus disease 2019 (COVID-19) infected individuals are biased due to a wide range of factors from testing access to concerns about missing low and non-symptomatic and self-tested individuals. Wastewater estimates offer an alternative to support community monitoring based on fecal shedding of the virus but are difficult to interpret when compared with the available public health data sets of infection rates. We examined all English literature until February 24, 2022, on Web of Science and PubMed with the terms [“seroprevalence” or “antibody”] AND [“COVID-19” or “SARS-CoV-2”] AND [“wastewater”]. We identified six studies. None of these studies considered randomized COVID-19 community anti-SARS-CoV-2 antibody testing paired with wastewater data.Added value of this studyThe study demonstrates how results from serial stratified randomized serological sampling of the community can be used to build a longitudinal model that can interpolate and extrapolate community levels of infection beyond specific testing dates. Such a model correlates well with wastewater concentrations indicating its utility as a surrogate for infection prevalence. The testing data used in the study were collected before wide availability of COVID-19 vaccines and are therefore unique as they are unlikely to include a significant number of false positive results.Implications of all the available evidenceThe study demonstrates that convenience sampling obtained data from health department reporting seriously underestimates community-wide prevalence of infection. In contrast, wastewater-based epidemiology may be a faster, cost-effective, and more robust method of estimating the prevalence of viral infections within specific urban areas.

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The emergence of a virus variant: dynamics of a competition model with cross-immunity time-delay validated by wastewater surveillance data for COVID-19

Pell

Brozak

Phan³

et al. 2023

J. Math. Biol.

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We consider the dynamics of a virus spreading through a population that produces a mutant strain with the ability to infect individuals that were infected with the established strain. Temporary cross-immunity is included using a time delay, but is found to be a harmless delay. We provide some sufficient conditions that guarantee local and global asymptotic stability of the disease-free equilibrium and the two boundary equilibria when the two strains outcompete one another. It is shown that, due to the immune evasion of the emerging strain, the reproduction number of the emerging strain must be significantly lower than that of the established strain for the local stability of the established-strain-only boundary equilibrium. To analyze the unique coexistence equilibrium we apply a quasi steady-state argument to reduce the full model to a two-dimensional one that exhibits a global asymptotically stable established-strain-only equilibrium or global asymptotically stable coexistence equilibrium. Our results indicate that the basic reproduction numbers of both strains govern the overall dynamics, but in nontrivial ways due to the inclusion of cross-immunity. The model is applied to study the emergence of the SARS-CoV-2 Delta variant in the presence of the Alpha variant using wastewater surveillance data from the Deer Island Treatment Plant in Massachusetts, USA.

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A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities

Cited by 78 publications

References 93 publications

Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program

Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program

Quantifying the relationship between sub-population wastewater samples and community-wide SARS-CoV-2 seroprevalence

The emergence of a virus variant: dynamics of a competition model with cross-immunity time-delay validated by wastewater surveillance data for COVID-19

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