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

WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, Jameel Institute, and Department of Mathematics, Imperial College London, in collaboration with the University of Sussex. 

Summary

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 of control strategies. We exten d the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt),to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. Our method can combine information across multiple locations and over time and was validated using 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 France respectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) times more transmissible than the wildtype (France data). All results are in line with previous estimates from literature, but could have been obtained earlier and more easily with our off-the-shelf open-source tool. Our tool can be used as an important first step towards quantifying the threat of new variants in real-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor the co-circulation and/or emergence of multiple variants of infectious pathogens.

The code for MV EpiEstim is open source: https://github.com/mrc-ide/EpiEstim/. In addition, information on how to run this new tool can be accessed here: https://github.com/mrc-ide/EpiEstim/blob/master/vignettes/MV_EpiEstim_vignette.Rmd