The reproduction number R_t in structured and nonstructured populations

DOI10.3934/MBE.2009.6.239MaRDI QIDQ2390594zbMATH OpenOpenAlexWikidataFDO

Authors Gerardo Chowell, Tom Burr

Publication date 30 July 2009

Published in Mathematical Biosciences and Engineering (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3934/mbe.2009.6.239

zbMATH Keywords

generation intervalstructured populations

Mathematics Subject Classification ID

Estimation in survival analysis and censored data (62N02) Probabilistic models, generic numerical methods in probability and statistics (65C20) Epidemiology (92D30)

Review text

Using daily counts of newly infected individuals, \textit{J. Wallinga} and \textit{P. Teunis} (WT) [Am. J. Epidem. 160, 500-516 (2004)] introduced a conceptually simple method to estimate the number of secondary cases per primary case for a given day. The method requires an estimate of the generation interval probability density function (pdf), which specifies the probabilities for the times between symptom onset in a primary case and symptom onset in a corresponding secondary case. Other methods to estimate are based on explicit models such as the SIR model; therefore, one might expect the WT method to be more robust to departures from SIR-type behavior. This paper uses simulated data to compare the quality of daily estimates based on a SIR model to those using the WT method for both structured (classical SIR assumptions are violated) and nonstructured (classical SIR assumptions hold) populations. By using detailed simulations that record the infection day of each new infection and the donor-recipient identities, the true and the generation interval pdf is known with negligible error. We find that the generation interval pdf is time dependent in all cases, which agrees with recent results reported elsewhere. We also find that the WT method performs essentially the same in the structured populations (except for a spatial network) as it does in nonstructured populations. And, the WT method does as well or better than a SIR-model based method in three of the four structured populations. Therefore, even if the contact patterns are heterogeneous as in the structured populations evaluated here, the WT method provides reasonable estimates, as does the SIR method.

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Cited in

(2)

• The daily computed weighted averaging basic reproduction number \(R_{0, k, \omega}^n\) for MERS-CoV in South Korea
• Estimating time-varying reproduction number by deep learning techniques

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