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Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2

By Jana S Huisman, Jeremie Scire, Daniel C. Angst, Richard A Neher, Sebastian Bonhoeffer, Tanja Stadler

Posted 30 Nov 2020
medRxiv DOI: 10.1101/2020.11.26.20239368

The effective reproductive number Re is a key indicator of the growth of an epidemic. Since the start of the SARS-CoV-2 pandemic, many methods and online dashboards have sprung up to monitor this number through time. However, these methods are not always thoroughly tested, correctly placed in time, or are overly confident during high incidence periods. Here, we present a method for near real time estimation of Re, applied to epidemic data from 170 countries. We thoroughly evaluate the method on simulated data, and present an intuitive web interface for interactive data exploration. We show that in the majority of countries the estimated Re dropped below 1 only after the introduction of major non-pharmaceutical interventions. For Europe the implementation of non-pharmaceutical interventions was broadly associated with reductions in the estimated Re. Globally though, relaxing non-pharmaceutical interventions had more varied effects on subsequent Re estimates. Our framework is useful to inform governments and the general public on the status of the epidemic in their country, and is used as the official source of Re estimates in Switzerland. It further allows detailed comparison between countries and in relation to covariates such as implemented public health policies, mobility, behaviour, or weather data.

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