Targeted maximum likelihood estimation of vaccine effectiveness and immune correlates in test-negative design studies with missing data

TL;DR

This paper introduces a targeted maximum likelihood estimation method for analyzing test-negative design studies, effectively handling missing data to assess vaccine effectiveness and immune correlates.

Contribution

It develops a semiparametric logistic regression approach that provides valid causal inference in TND studies with missing exposure data, improving confounding control.

Findings

Method performs well in simulations with missing data.

Application to COVID-19 vaccine data demonstrates practical utility.

Estimator is efficient and asymptotically linear.

Abstract

The test-negative design (TND) is a resource-efficient observational study design that can assess vaccine effectiveness and exposure-proximal immune correlates of disease. The TND enrolls symptomatic individuals seeking diagnostic testing and compares case status by an exposure variable, such as vaccination status or immune marker level, that is measured at testing. While the TND reduces confounding by healthcare-seeking behavior, other sources of confounding may remain. TND studies may also have missing data in the exposure variable due to incomplete records or two-phase sampling designs. We present a targeted maximum likelihood estimation approach involving a semiparametric logistic regression model that targets a causal conditional risk ratio of symptomatic disease in the healthcare-seeking population. Under causal and missing at random assumptions, our method produces an efficient, asymptotically linear estimator that provides flexible, data-driven confounding control and valid causal inference when analyzing TND studies with missing exposure variable data. We evaluate our method's finite sample properties using plasmode simulations of a two-phase TND immune correlates study. We also apply our method to assess COVID-19 vaccine effectiveness and antibody marker correlates of COVID-19 from TND study cohorts derived from the Moderna Coronavirus Efficacy phase 3 trial.