Use of Whole-Genome Sequencing to Estimate the Contribution of Immune Evasion and Waning Immunity on Decreasing COVID-19 Vaccine Effectiveness

Abstract

Background. The impact variant-specific immune evasion and waning protection have on declining coronavirus disease 2019 (COVID-19) vaccine effectiveness (VE) remains unclear. Using whole-genome sequencing (WGS), we examined the contribution these factors had on the decline that followed the introduction of the Delta variant. Furthermore, we evaluated calendar-period–based classification as a WGS alternative. Methods. We conducted a test-negative case-control study among people tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between 1 April and 24 August 2021. Variants were classified using WGS and calendar period. Results. We included 2029 cases (positive, sequenced samples) and 343 727 controls (negative tests). VE 14–89 days after second dose was significantly higher against Alpha (84.4%; 95% confidence interval [CI], 75.6%–90.0%) than Delta infection (68.9%; 95% CI, 58.0%–77.1%). The odds of Delta infection were significantly higher 90–149 than 14–89 days after second dose (P value = .003). Calendar-period–classified VE estimates approximated WGS-classified estimates; however, calendar-period–based classification was subject to misclassification (35% Alpha, 4% Delta). Conclusions. Both waning protection and variant-specific immune evasion contributed to the lower effectiveness. While calendar-period–classified VE estimates mirrored WGS-classified estimates, our analysis highlights the need for WGS when variants are cocirculating and misclassification is likely.