Emergence to dominance: Estimating time to dominance of SARS-CoV-2 variants using nonlinear statistical models

Relative proportion of cases in a multi-strain pandemic like the COVID-19 pandemic provides insight on how fast a newly emergent variant dominates the infected population. However, the behavior of relative proportion of emerging variants is an understudied field. We investigated the emerging behavior of dominant COVID-19 variants using nonlinear statistical methods and calculated the time to dominance of each variant.

We used a phenomenological approach to model national- and regional-level variant share data from the national genomic surveillance system provided by the Centers for Disease Control and Prevention to determine the best model to describe the emergence of two recent dominant variants of the SARS-CoV-2 virus: XBB.1.5 and JN.1. The proportions were modeled using logistic, Weibull, and generalized additive models. Model performance was evaluated using the Akaike Information Criteria (AIC) and the root mean square error (RMSE).

The Weibull model performed the worst out of all three approaches. The generalized additive model approach slightly outperformed the logistic model based on fit statistics, but lacked in interpretability compared to the logistic model. These models were then used to estimate the time elapsed from emergence to dominance in the infected population, denoted by the time to dominance (TTD). All three models yielded similar TTD estimates. The XBB.1.5 variant was found to dominate the population faster compared to the JN.1 variant, especially in HHS Region 2 (New York) where the XBB.1.5 was believed to emerge. This research expounds on how emerging viral strains transition to dominance, informing public health interventions against future emergent COVID-19 variants and other infectious diseases.