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

TL;DR

This paper introduces a simple logistic regression-based model to estimate and compare the contagiousness of SARS-CoV-2 variants, enabling real-time pandemic assessment without extensive sequencing.

Contribution

It presents a novel, invariant maximum likelihood estimation method for variant contagiousness, applied to Danish data, and demonstrates real-time forecasting of variant spread and reproduction numbers.

Findings

Alpha is 1.51 times more contagious than the ancestral variant.

Delta is 3.28 times more contagious than the ancestral variant.

Omicron is 3.15 times more infectious than Delta in vaccinated populations.

Abstract

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.