Preliminary modeling estimates of the relative transmissibility and immune escape of the Omicron SARS-CoV-2 variant of concern in South Africa

We develop a stochastic, multi-strain, compartmental epidemic model to estimate the relative transmissibility and immune escape of the Omicron variant of concern (VOC) in South Africa. The model integrates population, non-pharmaceutical interventions, vaccines, and epidemiological data and it is calibrated in the period May 1 ^st , 2021 – November 23 ^rd , 2021. We explore a parameter space of relative transmissibility with respect to the Delta variant and immune escape for Omicron by assuming an initial seeding, from unknown origin, in the first week of October 2021. We identify a region of the parameter space where combinations of relative transmissibility and immune escape are compatible with the growth of the epidemic wave. We also find that changes in the generation time associated with Omicron infections strongly affect the results concerning its relative transmissibility. The presented results are informed by current knowledge of Omicron and subject to changes.