AbstractOngoing infection with, and associated viral reproduction of, SARS-CoV-2 provides opportunities for the virus to acquire advantageous mutations, which may alter viral transmissibility and disease severity, and allow escape from natural or vaccine-derived immunity. The number of countries reporting Variants of Concern (VOCs) with such mutations continues to rise. Here, we investigate two scenarios for third waves of the COVID pandemic: one driven by increased transmissibility, and another driven by immune escape. We do this using three mathematical models: a parsimonious susceptible-latent-infectious-recovered (SEIR) deterministic model with homogeneous mixing, an age-structured SARS-CoV-2 transmission model and a stochastic importation model. We calibrated our models to the situation in England in May 2021, although the insights will generalise to other contexts. We therefore accurately captured infection dynamics and vaccination rates, and also used these to explore the potential impact of a putative new VOC-targeted vaccine. Epidemiological trajectories for putative VOCs are wide-ranging and heavily dependent on their transmissibility, immune escape capability, and the time at which a postulated VOC-targeted vaccine may be introduced. We demonstrate that a VOC with either a substantial transmission advantage over resident variants, or the ability to evade vaccine-derived and prior immunity, is expected to generate a wave of infections and hospitalisations comparable to those seen in the winter 2020-21 wave. Moreover, a variant that is less transmissible, but shows partial immune-escape could provoke a wave of infection that would not be revealed until control measures are further relaxed.
Cold Spring Harbor Laboratory