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We propose a simple dynamic model for estimating the relative contagiousnessof two virus variants. Maximum likelihood estimation and inference isconveniently invariant to variation in the total number of cases over thesample period and can be expressed as a logistic regression. We apply the modelto Danish SARS-CoV-2 variant data. We estimate the reproduction numbers ofAlpha and Delta to be larger than that of the ancestral variant by a factor of1.51 [CI 95%: 1.50, 1.53] and 3.28 [CI 95%: 3.01, 3.58], respectively. In apredominately vaccinated population, we estimate Omicron to be 3.15 [CI 95%:2.83, 3.50] times more infectious than Delta. Forecasting the proportion of anemerging virus variant is straight forward and we proceed to show how theeffective reproduction number for a new variant can be estimated withoutcontemporary sequencing results. This is useful for assessing the state of thepandemic in real time as we illustrate empirically with the inferred effectivereproduction number for the Alpha variant.

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