Joint estimation of the basic reproduction number and serial interval using Sequential Bayes

TL;DR

This paper introduces a Bayesian sequential approach for real-time joint estimation of the basic reproduction number and serial interval from case data, improving accuracy and stability over existing likelihood-based methods.

Contribution

It develops a novel Bayesian framework with a linked prior for $R_0$ and SI, enabling sequential updating and better estimates during outbreaks.

Findings

More precise and stable $R_0$ estimates compared to existing methods.

Reliable serial interval estimates when prior info is accurate.

Effective real-time inference demonstrated with COVID-19 data.

Abstract

Early in an infectious disease outbreak, timely and accurate estimation of the basic reproduction number ($R_0$) and the serial interval (SI) is critical for understanding transmission dynamics and informing public health responses. While many methods estimate these quantities separately, and a small number jointly estimate them from incidence data, existing joint approaches are largely likelihood-based and do not fully exploit prior information. We propose a novel Bayesian framework for the joint estimation of $R_0$ and the serial interval using only case count data, implemented through a sequential Bayes approach. Our method assumes an SIR model and employs a mildly informative joint prior constructed by linking log-Gamma marginal distributions for $R_0$ and the SI via a Gaussian copula, explicitly accounting for their dependence. The prior is updated sequentially as new incidence data become available, allowing for real-time inference. We assess the performance of the proposed estimator through extensive simulation studies under correct model specification as well as under model misspecification, including when the true data come from an SEIR or SEAIR model, and under varying degrees of prior misspecification. Comparisons with the widely used White and Pagano likelihood-based joint estimator show that our approach yields substantially more precise and stable estimates of $R_0$, with comparable or improved bias, particularly in the early stages of an outbreak. Estimation of the SI is more sensitive to prior misspecification; however, when prior information is reasonably accurate, our method provides reliable SI estimates and remains more stable than the competing approach. We illustrate the practical utility of the proposed method using Canadian COVID-19 incidence data at both national and provincial levels.