Use of Rapid Genomic Sequencing and Vaccine Effectiveness to Assess Vaccine Match Against a New Subgroup of Influenza A(H3N2) Viruses — Michigan, 2021
Four human influenza viruses circulate currently, requiring annual vaccine updates to match rapid viral evolution. However, vaccine effectiveness (VE) estimates against contemporary viruses are typically unavailable before annual vaccine strain selection in February. On November 10, 2021, University of Michigan reported a sharp increase in influenza A(H3N2) patients marking one of the first large-scale U.S. influenza outbreaks during SARS-CoV-2 cocirculation. We conducted a field investigation to genetically characterize and estimate effectiveness of the 2021–2022 influenza vaccine against circulating A(H3N2) viruses.
Symptomatic university clinic patients were tested for influenza by molecular assay. Influenza viruses were genetically characterized using Next Generation Sequencing (NGS). Vaccination status was determined using immunization registries. We estimated VE as (1 minus odds ratio) × 100, adjusted for age and race/ethnicity, using logistic regression comparing odds of vaccination (≥ 14 days before influenza testing) among influenzapositive vs influenza-negative patients.
During October 6–November 12, 481 of 2,405 patients (20%) tested positive for influenza A(H3N2). One patient was hospitalized. Median age of influenza patients was 19 years (range: 17–29). All 386 sequenced viruses belonged to an emergent A(H3N2) 2a.2 subgroup, which was antigenically distinguishable from the A(H3N2) virus in the 2021–2022 vaccine. Vaccination rates were similar between influenza-positive (27%) and influenzanegative patients (27%). VE against 2a.2 circulating viruses was -4% (95% CI: -31%–18%). Results were provided to state authorities on November 19.
This novel field investigation pairing NGS and VE early in the season, before the annual vaccine strain selection, showed influenza vaccination was ineffective against illness in young adults from an emergent A(H3N2) virus. Results guided communication of prevention and treatment measures, including encouraging symptomatic persons to isolate and promoting influenza antiviral treatment. Rapid sequencing coupled with VE analyses before annual vaccine strain selection decisions might improve influenza control efforts.