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 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 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 o -the-shelf open-source tool.
Our tool can be used as an important rst 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.