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  4. Computing the daily reproduction number of COVID-19 by inverting the renewal equation using a variational technique
 
research article

Computing the daily reproduction number of COVID-19 by inverting the renewal equation using a variational technique

Alvarez, Luis
•
Colom, Miguel
•
Morel, Jean-David  
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December 14, 2021
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS)

The COVID-19 pandemic has undergone frequent and rapid changes in its local and global infection rates, driven by governmental measures or the emergence of new viral variants. The reproduction number Rt indicates the average number of cases generated by an infected person at time t and is a key indicator of the spread of an epidemic. A timely estimation of R-t is a crucial tool to enable governmental organizations to adapt quickly to these changes and assess the consequences of their policies. The EpiEstimmethod is themostwidely accepted method for estimating R-t. But it estimates R-t with a significant temporal delay. Here, we propose a method, EpiInvert, that shows good agreement with EpiEstim, but that provides estimates of R-t several days in advance. We show that R-t can be estimated by inverting the renewal equation linking R-t with the observed incidence curve of new cases, i(t). Our signal-processing approach to this problem yields both R-t and a restored i(t) corrected for the "weekend effect" by applying a deconvolution and denoising procedure. The implementations of the EpiInvert and EpiEstim methods are fully open source and can be run in real time on every country in the world and every US state.

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Type
research article
DOI
10.1073/pnas.2105112118
Web of Science ID

WOS:000732715700019

Author(s)
Alvarez, Luis
Colom, Miguel
Morel, Jean-David  
Morel, Jean-Michel
Date Issued

2021-12-14

Publisher

National Academy of Sciences

Published in
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS)
Volume

118

Issue

50

Article Number

e2105112118

Subjects

Multidisciplinary Sciences

•

Science & Technology - Other Topics

•

covid-19

•

renewal equation

•

reproduction number

•

integral equations

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LISP  
Available on Infoscience
January 1, 2022
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/184196
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