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Predicting the Effectiveness of Population Replacement Strategy Using Mathematical Modeling
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Time-varying reproductive number estimation for practical application in structured populations.

Erin Clancey1, Eric T Lofgren1

  • 1Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA.

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|August 29, 2025
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Summary

EpiEstim's real-time estimates of the time-varying reproductive number (ℛ t) can be temporally biased in structured populations. Adjusting methods can recover accuracy for epidemic response.

Keywords:
EpiEstimgeneration interval distributionpopulation structuresimulationtime-varying reproductive number

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Area of Science:

  • Epidemiology
  • Statistical modeling
  • Computational biology

Background:

  • The time-varying reproductive number (ℛ t) is crucial for real-time epidemic assessment.
  • The EpiEstim framework provides estimates for ℛ t but its performance in structured populations is under-evaluated.
  • Population structure can introduce temporal biases in ℛ t estimates.

Purpose of the Study:

  • To evaluate the temporal performance of EpiEstim in small, non-randomly mixing populations.
  • To assess the impact of population structure on ℛ t estimates.
  • To demonstrate a method for correcting temporal biases in EpiEstim ℛ t estimates.

Main Methods:

  • Simulated COVID-19 outbreak data from a two-population mechanistic model.
  • Comparison of true ℛ t with EpiEstim-derived ℛ ˆ t estimates.
  • Analysis of temporal bias by comparing time points when ℛ t crosses the critical threshold of 1.

Main Results:

  • EpiEstim ℛ ˆ t estimates prematurely fell below 1 in structured populations.
  • Weekly aggregated data showed later ℛ ˆ t threshold crossings than daily data, with population structure having no additional effect.
  • Recovering temporal accuracy was achieved by using lagging subpopulation data for total population ℛ ˆ t estimation.

Conclusions:

  • Population structure can bias EpiEstim ℛ t estimates near the critical threshold.
  • Prudent application of EpiEstim to structured population data is necessary for accurate epidemic response.
  • Methods exist to mitigate temporal biases in ℛ t estimation within structured populations.