Estimation of local time-varying reproduction numbers in noisy surveillance data

  1. Wenrui Li
  2. Katia Bulekova
  3. Brian Gregor
  4. Laura F. White
  5. Eric D. Kolaczyk

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Abstract

A valuable metric in understanding local infectious disease dynamics is the local time-varying reproduction number, i.e. the expected number of secondary local cases caused by each infected individual. Accurate estimation of this quantity requires distinguishing cases arising from local transmission from those imported from elsewhere. Realistically, we can expect identification of cases as local or imported to be imperfect. We study the propagation of such errors in estimation of the local time-varying reproduction number. In addition, we propose a Bayesian framework for estimation of the true local time-varying reproduction number when identification errors exist. And we illustrate the practical performance of our estimator through simulation studies and with outbreaks of COVID-19 in Hong Kong and Victoria, Australia.

This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’.

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  1. Version published to 10.1098/rsta.2021.0303
  2. Version published to 10.1101/2021.04.23.21255958v3 on medRxiv
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    SciScore for 10.1101/2021.04.23.21255958: (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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  4. Version published to 10.1101/2021.04.23.21255958v2 on medRxiv
  5. Version published to 10.1101/2021.04.23.21255958v1 on medRxiv