Intraseason decline in influenza vaccine effectiveness during the 2016 southern hemisphere influenza season: A test-negative design study and phylogenetic assessment

Abstract Background We estimated the effectiveness of seasonal inactivated influenza vaccine and the potential influence of timing of immunization on vaccine effectiveness (VE) using data from the 2016 southern hemisphere influenza season. Methods Data were pooled from three routine syndromic sentinel surveillance systems in general practices in Australia. Each system routinely collected specimens for influenza testing from patients presenting with influenza-like illness. Next generation sequencing was used to characterize viruses. Using a test-negative design, VE was estimated based on the odds of vaccination among influenza-positive cases as compared to influenza-negative controls. Subgroup analyses were used to estimate VE by type, subtype and lineage, as well as age group and time between vaccination and symptom onset. Results A total of 1085 patients tested for influenza in 2016 were included in the analysis, of whom 447 (41%) tested positive for influenza. The majority of detections were influenza A/H3N2 (74%). One-third (31%) of patients received the 2016 southern hemisphere formulation influenza vaccine. Overall, VE was estimated at 40% (95% CI: 18–56%). VE estimates were highest for patients immunized within two months prior to symptom onset (VE: 60%; 95% CI: 26–78%) and lowest for patients immunized >4 months prior to symptom onset (VE: 19%; 95% CI: −73–62%). Discussion Overall, the 2016 influenza vaccine showed good protection against laboratory-confirmed infection among general practice patients. Results by duration of vaccination suggest a significant decline in effectiveness during the 2016 influenza season, indicating immunization close to influenza season offered optimal protection.