Estimated BNT162b2 Vaccine Effectiveness Against Infection With Delta and Omicron Variants Among US Children 5 to 11 Years of Age.

Importance: Data describing the vaccine effectiveness (VE) and durability of BNT162b2 among children 5 to 11 years of age are needed. Objective: To estimate BNT162b2 VE against SARS-CoV-2 infection among children aged 5 to 11 years during Delta and Omicron variant-predominant periods and to further assess VE according to prior SARS-CoV-2 infection status and by sublineage during the Omicron variant-predominant period. Design, Setting, and Participants: This test-negative case-control study was conducted from November 2 to December 9, 2021 (Delta variant), and from January 16 to September 30, 2022 (Omicron variant), among 160 002 children tested at a large national US retail pharmacy chain, for SARS-CoV-2 via polymerase chain reaction (PCR); 62 719 children were tested during the Delta period, and 97 283 were tested during the Omicron period. Exposure: Vaccination with BNT162b2 before SARS-CoV-2 testing vs no vaccination. Main Outcomes and Measures: The primary outcome was SARS-CoV-2 infection confirmed by PCR (regardless of the presence of symptoms), and the secondary outcome was confirmed symptomatic infection. Adjusted estimated VE was calculated from multilevel logistic regression models. Results: A total of 39 117 children tested positive and 131 686 tested negative for SARS-CoV-2 (total, 170 803; 84 487 [49%] were boys; mean [SD] age was 9 [2] years; 74 236 [43%] were White non-Hispanic or non-Latino; and 37 318 [22%] were Hispanic or Latino). Final VE analyses included 160 002 children without SARS-CoV-2 infection less than 90 days prior. The VE of 2 doses of BNT162b2 against Delta was 85% (95% CI, 80%-89%; median follow-up, 1 month) compared with the Omicron period (20% [95% CI, 17%-23%]; median follow-up, 4 months). The adjusted VE of 2 doses against Omicron at less than 3 months was 39% (95% CI, 36%-42%), and at 3 months or more, it was -1% (95% CI, -6% to 3%). Protection against Omicron was higher among children with vs without infection 90 days or more prior but decreased in all children approximately 3 months after the second dose (58% [95% CI, 49%-66%] with infection vs 37% [95% CI, 34%-41%] without infection at <3 months; 27% [95% CI, 17%-35%] with infection vs -7% [95% CI, -12% to -1%] at ≥3 months without infection). The VE of 2 doses of BNT162b2 at less than 3 months by Omicron sublineage was 40% (95% CI, 36%-43%) for BA.1, 32% (95% CI, 21%-41%) for BA.2/BA.2.12.1, and 50% (95% CI, 37%-60%) for BA.4/BA.5. After 3 months or more, VE was nonsignificant for BA.2/BA.2.12.1 and BA.4/BA.5. The VE of a booster dose was 55% (95% CI, 50%-60%) against Omicron, with no evidence of waning at 3 months or more. Conclusions and Relevance: This study suggests that, among children aged 5 to 11 years, 2 doses of BNT162b2 provided modest short-term protection against Omicron infection that was higher for those with prior infection; however, VE waned after approximately 3 months in all children. A booster dose restored protection against Omicron and was maintained for at least 3 months. These findings highlight the continued importance of booster vaccination regardless of history of prior COVID-19.

Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants.

SARS-CoV-2, the virus that causes COVID-19, has many variants capable of rapid transmission causing serious illness. Timely surveillance of new variants is essential for an effective public health response. Ensuring availability and access to diagnostic and molecular testing is key to this type of surveillance. This study utilized reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing results from COVID-19-positive patient samples obtained through a collaboration between Aegis Sciences Corporation and Walgreens Pharmacy that has conducted more than 8.5 million COVID-19 tests at ~5,200 locations across the United States and Puerto Rico. Viral evolution of SARS-CoV-2 can lead to mutations in the S-gene that cause reduced or failed S-gene amplification in diagnostic PCR tests. These anomalies, labeled reduced S-gene target performance (rSGTP) and S-gene target failure (SGTF), are characteristic of variants carrying the del69-70 mutation, such as Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages. This observation has been validated by whole genome sequencing and can provide presumptive lineage data following completion of diagnostic PCR testing in 24-48 hours from collection. Active surveillance of trends in PCR and sequencing results is key to the identification of changes in viral transmission and emerging variants. This study shows that rSGTP and SGTF can be utilized for near real-time tracking and surveillance of SARS-CoV-2 variants, and is superior to the use of SGTF alone due to the significant proportion of Alpha and Omicron (B.1.1.529, BA.1, and BA.1.1) lineages known to carry the del69-70 mutation and observed to have S-gene amplification. Adopting new tools and techniques to both diagnose acute infections and expedite identification of emerging variants is critical to supporting public health.