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Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19

Yang, X. L., Wang, S. J., Xing, Y. L. , Li, Ling ORCID: 0000-0002-4026-0216, Xu, R., Friston, K. J. & Guo, Y. (2022). Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19. PLoS Computational Biology, 18(2), article number e1009807. doi: 10.1371/journal.pcbi.1009807


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.

Author summary
Monitoring the evolution of transmission dynamics is of great importance in response to the COVID-19 pandemic. The transmission dynamics of infectious disease is described by epidemiological models, but the model parameters may vary substantially due to differences in government intervention policies. Existing methods on estimating time-varying epidemiological parameters face problems such as lagging observation, averaging inference, and unreliable uncertainty. To address these issues, we have proposed the Bayesian data framework to provide a timely estimate with credibility interval. We have developed the ‘DARt’ system to monitor the instantaneous reproduction number Rt from daily COVID-19 reports. The accuracy and robustness of our system are validated in numerical simulations and in retrospective analyses of real-world scenarios. Our system provides the insights of impacts of different intervention polices and highlights the effectiveness of undergoing mass vaccination.

Publication Type: Article
Additional Information: © 2022 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Subjects: H Social Sciences > HA Statistics
H Social Sciences > HN Social history and conditions. Social problems. Social reform
Q Science > QA Mathematics
Q Science > QR Microbiology > QR180 Immunology
R Medicine > RA Public aspects of medicine > RA0421 Public health. Hygiene. Preventive Medicine
Departments: School of Science & Technology > Engineering
SWORD Depositor:
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Available under License Creative Commons: Attribution International Public License 4.0.

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