Validating and leveraging non-SARS-CoV-2 respiratory infection as a negative control outcome in a phase 3 COVID-19 vaccine trial with extended observational follow-up.

Negative control outcomes (NCOs) are useful tools for hidden bias detection, but empirical evidence validating NCOs for COVID-19 is lacking. To address this gap, we examined the blinded phase of the randomized, placebo-controlled Coronavirus Vaccine Efficacy (COVE; NCT04470427) trial of the mRNA-1273 COVID-19 vaccine. We confirmed that acute respiratory illness with a positive test for a non-SARS-CoV-2 respiratory pathogen on a multiplex PCR panel was a valid NCO for COVID-19, considering that it was unaffected by vaccination (vaccine efficacy, VE = 3.3% (95% CI, -22.3 to 23.6)) yet strongly associated with COVID-19 (odds ratio = 2.95 (95% CI, 2.00, 4.24)). Subsequently, we leveraged non-SARS-CoV-2 infections to detect bias in time-varying VE estimates from COVE's blinded and booster phases. Balanced incidence of non-SARS-CoV-2 infection between vaccinated and unvaccinated COVID-19-free risk sets suggested low selection bias in VE estimates of two-dose mRNA-1273 against COVID-19 during the blinded phase (VE = 92.5% (95% CI, 88.8, 94.9) 14 days post-dose-two, stable for 5 months). In COVE's booster phase, higher non-SARS-CoV-2 incidence was observed after the single booster (intensity ratio, IR = 2.38 (95% CI, 1.75, 3.25) 14 days post-boost), suggesting that booster VE estimates may underestimate the true VE against COVID-19. Our findings demonstrate the potential of off-target infections for unraveling complex biases in COVID-19 vaccine studies. Trial registration: NCT04470427, https://clinicaltrials.gov/study/NCT04470427.