Relative contagiousness of emerging virus variants: An analysis of the Alpha, Delta, and Omicron SARS-CoV-2 variants
提出一个简单动态模型来估计两种病毒变种的相对传染性，应用于丹麦SARS-CoV-2变种数据，发现阿尔法和德尔塔的再生数比原始变种分别高1.51和3.28倍，奥密克戎比德尔塔高3.15倍。
Summary 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. We apply the model to Danish SARS-CoV-2 variant data. We estimate the reproduction numbers of Alpha and Delta to be larger than that of the ancestral variant by a factor of 1.51 [CI 95%: 1.50, 1.53] and 3.28 [CI 95%: 3.01, 3.58], respectively. In a predominately vaccinated population, we estimate Omicron to be 3.15 [CI 95%: 2.83, 3.50] times more infectious than Delta. Forecasting the proportion of an emerging virus variant is straight forward and we proceed to show how the effective reproduction number for a 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.