Imperial College London
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DrAnneCori

Faculty of Medicine, School of Public Health

Senior Lecturer in Infectious Disease Modelling
 
 
 
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Contact

 

+44 (0)20 7594 3229a.cori

 
 
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Location

 

404School of Public HealthWhite City Campus

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Summary

 

Publications

Citation

BibTex format

@techreport{Bhatia:2021,
author = {Bhatia, S and Wardle, J and Nash, R and Nouvellet, P and Cori, A},
title = {Report 47: A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study},
url = {https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2021-11-26-COVID19-Report-47.pdf},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - RPRT
AB  - Recent months have demonstrated that emerging variants may set back the global COVID-19 response.The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation ofcontrol strategies.We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt),to estimate in real-time the e ective transmission advantage of a new variant compared to a referencevariant. Our method can combine information across multiple locations and over time and was validatedusing an extensive simulation study, designed to mimic a variety of real-time epidemic contexts.We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29,(95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and Francerespectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) timesmore transmissible than the wildtype (France data). All results are in line with previous estimates fromliterature, but could have been obtained earlier and more easily with our o -the-shelf open-source tool.Our tool can be used as an important  rst step towards quantifying the threat of new variants inreal-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor theco-circulation and/or emergence of multiple variants of infectious pathogens.
AU  - Bhatia,S
AU  - Wardle,J
AU  - Nash,R
AU  - Nouvellet,P
AU  - Cori,A
PY  - 2021///
TI  - Report 47: A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study
UR  - https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2021-11-26-COVID19-Report-47.pdf
UR  - http://hdl.handle.net/10044/1/92689
ER  -
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