Estimating the basic reproduction number at the beginning of an outbreak under incomplete data

Abstract

AbstractWe compare different methods of estimating the basic reproduction number, R0, focusing on the early stages of an epidemic, and considering weekly reports of new infecteds. We study three standard epidemiological models: SIR, SEIR, and SEAIR and examine the sensitivity of the estimators to the model structure. As some methods are developed assuming specific epidemiological models, our work adds a study of their performance in both the well- and miss-specified settings. We focus on parameters matching various types of respiratory viruses, although the general approach is easily extendable to other scenarios.