Temporal Properties of Vaccine Effectiveness Measures in Presence of Multiple Pathogen Variants and Multiple Vaccines

Abstract: Vaccine effectiveness (VE) is typically defined as incidence rate ratio, cumulative-risk ratio, or odds ratio. The VE based on incidence rate ratio is known to be time-invariant over the study period for leaky action vaccines and, the VE based on cumulative-risk ratio is time-invariant for all-or-none action vaccines. Consequently, these VE measures are recommended as appropriate measures of VE for leaky and all-or-none vaccines, respectively. However, in diseases with multiple pathogen variants and multiple vaccines, investigators may also be interested in variant-specific VE of a vaccine, the relative VE of a vaccine against two variants, or the relative VE of different vaccines against a given variant. In this multi-variant and multi-vaccine scenario, the temporal properties of the aforementioned VE measures have not been studied entirely yet. Furthermore, no general-purpose sample size calculator is available for either studies that intend to estimate variant-specific VE or relative VE. As a solution, we define variant-specific and relative VE measures while accounting for multiple competing pathogen variants. We then propose a generic mode of action for all-or-none vaccines in a multi-variant setting. Subsequently, we evaluate the conditions and the extent to which various VE measures can be time-varying. We show that every VE measure is time-varying for all-or-none action vaccines in a multi-variant and multi-vaccine scenario. For leaky vaccines, we show that all measures other than those based on incidence rate ratios are time-varying. We discuss the practical implications of these results on VE studies in the context of the commonly used cohort, cumulative case-control, and test-negative study designs. Lastly, for the multi-variant and multi-vaccine scenario, we implement sample size calculations for both variant-specific and relative VE in an R package and an online calculator.