Relative Contagiousness of Emerging Virus Variants: An Analysis of SARS-CoV-2 Alpha and Delta Variants

We propose a simple dynamic model for estimating the relative contagiousness of two virus variants. Maximum likelihood estimation and inference is conveniently invariant to variation in the total number of cases over the sample period and can be expressed as a logistic regression. Using weekly Danish data we estimate the Alpha variant of SARS-CoV-2 to increase the reproduction number by a factor of 1.51 [CI 95%: 1.50, 1.53] relative to the ancestral variant. The Delta variant increases the reproduction number by a factor of 2.17 [CI 95%: 1.99, 2.36] relative to the Alpha variant and a factor of 3.28 [CI 95%: 3.01, 3.58] relative to the ancestral variant. Forecasting the proportion of an emerging virus variant is straight forward and we proceed to show how the effective reproduction number for the new variant can be estimated without contemporary sequencing results. This is useful for assessing the state of the pandemic in real time as we illustrate empirically with the inferred effective reproduction number for the Alpha variant.