Abstract
Background:Assessing temporal variations in transmission in different countries is essential for monitoring the epidemic, evaluating the effectiveness of public health interventions and estimating the impact of changes in policy.Methods:We use case and death notification data to generate daily estimates of the time-varying reproduction number globally, regionally, nationally, and subnationally over a 12-week rolling window. Our modelling framework, based on open source tooling, accounts for uncertainty in reporting delays, so that the reproduction number is estimated based on underlying latent infections.Results:Estimates of the reproduction number, trajectories of infections, and forecasts are displayed on a dedicated website as both maps and time series, and made available to download in tabular form.Conclusions: This decision-support tool can be used to assess changes in virus transmission both globally, regionally, nationally, and subnationally. This allows public health officials and policymakers to track the progress of the outbreak in near real-time using an epidemiologically valid measure. As well as providing regular updates on our website, we also provide an open source tool-set so that our approach can be used directly by researchers and policymakers on confidential data-sets. We hope that our tool will be used to support decisions in countries worldwide throughout the ongoing COVID-19 pandemic.
Highlights
The coronavirus disease 2019 (COVID-19) pandemic that emerged in December 2019 has since spread to over 100 countries in every continent except Antarctica
As well as providing regular updates on our website, we provide an open source tool-set so that our approach can be used directly by researchers and policymakers on confidential data-sets
We hope that our tool will be used to support decisions in countries worldwide throughout the ongoing COVID-19 pandemic
Summary
The coronavirus disease 2019 (COVID-19) pandemic that emerged in December 2019 has since spread to over 100 countries in every continent except Antarctica. A method for tracking the progress of an outbreak is to measure changes in the time-varying reproduction number (effective reproduction number), which represents the average number of secondary infections generated by each new infectious case[6,7,8]. This approach can be advantageous compared to monitoring numbers of newly reported or symptomatic cases since, in principle, reproduction number estimates reflect variations in transmission intensity. Monitoring changes in the time-varying reproduction can account for this delay and reveals variations in transmissibility that are not clear when using only reported cases. Assessing temporal variations in transmission in different countries is essential for monitoring the epidemic, evaluating the effectiveness of public health interventions and estimating the impact of changes in policy
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