Predicting Overall Vaccine Efficacy in a New Setting by Re-calibrating Baseline Covariate and Intermediate Response Endpoint Effect Modifiers of Type-Specific Vaccine Efficacy

Abstract

Abstract We develop a transport formula for predicting overall cumulative vaccine efficacy through time t (VE(t)$$VE(t)$$) to prevent clinically significant infection with a genetically diverse pathogen (e. g., HIV infection) in a new setting for which a Phase III preventive vaccine efficacy trial that would directly estimate VE(t)$$VE(t)$$ has not yet been conducted. The formula integrates data from (1) a previous Phase III trial, (2) a Phase I/II immune response biomarker endpoint trial in the new setting where a follow-up Phase III trial is planned, (3) epidemiological data on background HIV infection incidence in the new setting; and (4) genomic epidemiological data on HIV sequence distributions in the previous and new settings. For (1), the randomized vaccine versus placebo Phase III trial yields estimates of vaccine efficacy to prevent particular genotypes of HIV in participant subgroups defined by baseline covariates X and immune responses to vaccination S(1)$$S(1)$$ measured at a fixed time point τ$$\tau $$ (potential outcomes if assigned vaccine); often one or more immune responses to vaccination are available that modify genotype-specific vaccine efficacy. The formula focuses on subgroups defined by X and S(1)$$S(1)$$ and being at-risk for HIV infection at τ$$\tau $$ under both the vaccine and placebo treatment assignments. For (2), the Phase I/II trial tests the same vaccine in a new setting, or a refined new vaccine in the same or new setting, and measures the same baseline covariates and immune responses as the original Phase III trial. For (3), epidemiological data in the new setting are used to project overall background HIV infection rates in the baseline covariate subgroups in the planned Phase III trial, hence re-calibrating for HIV incidence differences in the two settings; whereas for (4), data bases of HIV sequences measured from HIV infected individuals are used to re-calibrate for differences in the distributions of the circulating HIV genotypes in the two settings. The transport formula incorporates a user-specified bridging assumption function that measures differences in HIV genotype-specific conditional biological-susceptibility vaccine efficacies in the two settings, facilitating a sensitivity analysis. We illustrate the transport formula with application to HIV Vaccine Trials Network (HVTN) research. One application of the transport formula is to use predicted VE(t)$$VE(t)$$ as a rational criterion for ranking a set of candidate vaccines being studied in Phase I/II trials for their priority for down-selection into the follow-up Phase III trial.