Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program
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Abstract
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 10 12 (virus particles per 100,000 persons per day) in the epidemic trough in August 2020 to almost 10 15 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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SciScore for 10.1101/2022.05.25.22275569: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The two approaches serve different purposes, and each has its strengths and limitations. A main strength of the mechanistic modelling is that all parameters have a biological interpretation, and that these analyses can be used for scenario studies. The results from such analyses, however, depend critically on model assumptions and are surrounded with large uncertainties. Our analyses do not yield a mechanistic interpretation but give …
SciScore for 10.1101/2022.05.25.22275569: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The two approaches serve different purposes, and each has its strengths and limitations. A main strength of the mechanistic modelling is that all parameters have a biological interpretation, and that these analyses can be used for scenario studies. The results from such analyses, however, depend critically on model assumptions and are surrounded with large uncertainties. Our analyses do not yield a mechanistic interpretation but give precise estimates of latent virus loads that arguably are less dependent on specific model assumptions. In ongoing work, we aim to merge the two approaches by fitting transmission models at a local scale using generalized profiling [26]. Since the infrastructure of receiving sewage samples are in place, the detection of other viruses can be added to the Dutch sewage surveillance program. These might include rotavirus and enteroviruses but also influenza viruses [27, 28], thus providing a comprehensive surveillance tool for pandemic preparedness. Moreover, sewage surveillance for antimicrobial resistance has already shown its potential [29]. In principle, our methods of analysis can directly be applied to other targets and can deal with noise and unbalanced data in a principled manner. The SARS-CoV-2 sewage surveillance program in the Netherlands has contributed to integrating available sewage data in a coherent framework, and also to informing the Dutch government on national and regional trends in SARS-COV-2 circulation [30]. Specifically, data ...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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Results from scite Reference Check: We found no unreliable references.
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