ArticlePLoS computational biology2022
Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Data-driven strategies for model-informed decision-making during the COVID-19 pandemic: a systematic review.BMJ open · 2026Pooled it
- Enhancing time-varying reproduction number estimates for COVID-19 with behavior and surveillance data in South Korea, 2020-2022.Archives of public health = Archives belges de sante publique · 2026Article
- Data assimilation for estimating time-varying reproduction numbers.Journal of the Royal Society, Interface · 2025Article
- Robust uncertainty quantification in popular estimators of the instantaneous reproduction number.American journal of epidemiology · 2025Article
- A Primer on Inference and Prediction With Epidemic Renewal Models and Sequential Monte Carlo.Statistics in medicine · 2025Article
- A novel approach to estimatingFrontiers in public health · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Estimating the changes of epidemiological parameters, such as instantaneous reproduction number, Rt, is important for understanding the transmission dynamics of infectious diseases. Current estimates of time-varying epidemiological parameters often face problems such as lagging observations, averaging inference, and improper quantification of uncertainties. To address these problems, we propose a Bayesian data assimilation framework for time-varying parameter estimation. Specifically, this framework is applied to estimate the instantaneous reproduction number Rt during emerging epidemics, resulting in the state-of-the-art 'DARt' system. With DARt, time misalignment caused by lagging observations is tackled by incorporating observation delays into the joint inference of infections and Rt; the drawback of averaging is overcome by instantaneously updating upon new observations and developing a model selection mechanism that captures abrupt changes; the uncertainty is quantified and reduced by employing Bayesian smoothing. We validate the performance of DARt and demonstrate its power in describing the transmission dynamics of COVID-19. The proposed approach provides a promising solution for making accurate and timely estimation for transmission dynamics based on reported data.
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Registered trials
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