EpiLPS: a fast and flexible Bayesian tool for near real-time estimation of the time-varying reproduction number (preprint)

ABSTRACT

In infectious disease epidemiology, the instantaneous reproduction number R ( t ) is a timevarying metric defined as the average number of secondary infections generated by individuals who are infectious at time t . It is therefore a crucial epidemiological parameter that assists public health decision makers in the management of an epidemic. We present a new Bayesian tool for robust estimation of the time-varying reproduction number. The proposed methodology smooths the epidemic curve and allows to obtain (approximate) point estimates and credible envelopes of R ( t ) by employing the renewal equation, using Bayesian P-splines coupled with Laplace approximations of the conditional posterior of the spline vector. Two alternative approaches for inference are presented (1) an approach based on a maximum a posteriori argument for the model hyperparameters, delivering estimates of R ( t ) in only a few seconds; and (2) an approach based on a MCMC scheme with underlying Langevin dynamics for efficient sampling of the posterior target distribution. Case counts per unit of time are assumed to follow a Negative Binomial distribution to account for potential excess variability in the data that would not be captured by a classic Poisson model. Furthermore, after smoothing the epidemic curve, a “plug-in” estimate of the reproduction number can be obtained from the renewal equation yielding a closed form expression of R ( t ) as a function of the spline parameters. The approach is extremely fast and free of arbitrary smoothing assumptions. EpiLPS is applied on data of SARS-CoV-1 in Hong-Kong (2003), influenza A H1N1 (2009) in the USA and current SARS-CoV-2 pandemic (2020-2021) for Belgium, Portugal, Denmark and France. Author summary The instantaneous reproduction number R ( t ) is a key metric that provides important insights into an epidemic outbreak. We present a flexible Bayesian approach called EpiLPS (Epidemiological modeling with Laplacian-P-splines) for smooth estimation of the epidemic curve and R ( t ). Computational speed and absence of arbitrary assumptions on smoothing makes EpiLPS an interesting tool for near real-time estimation of the reproduction number. An R software package is available ( https//github.com/oswaldogressani ).