Genomic and Clinical Analysis of Influenza A in Hospitalized Adults, 2019–2024: Exploratory Evidence on Neuraminidase and Polymerase Acidic Protein Mutation‐Outcome Associations From a Single Center

BACKGROUND: Antivirals are widely used to treat influenza, but potential resistance mutations remain a major challenge, and clinical data on key resistance mutations are limited. METHODS: We conducted a retrospective cohort study of 765 adults with RT-PCR-confirmed influenza A admitted to Ruijin Hospital, Shanghai, between 2019 and 2024 to determine whether specific NA/PA mutations are associated with severe outcomes or prolonged length of stay (LOS) when analyzed alongside key host factors. PA and NA sequences were obtained and linked to the clinical cohort for mutation-clinical outcome analyses. Multiple testing was addressed by controlling the false discovery rate using the Benjamini-Hochberg procedure. RESULTS: Among 765 inpatients with influenza A virus infection, the median age was 68 years; 5.0% were severe disease and 9.9% died. Older age, higher CURB-65 score, and bacterial/fungal co-infection were the main correlates of mortality, whereas antiviral regimen and Ct value were not independently associated with mortality or severe outcomes. Adjusted observational analyses showed a lower estimate for severe disease with baloxavir but no association with in-hospital death. Major high-level resistance mutations were absent; detected NA/PA mutations showed no robust association with severe disease or mortality. PA-F105L showed an exploratory association with longer LOS, but this finding was attenuated after adjustment and was confounded by clade and calendar period. CONCLUSIONS: Clinical outcomes were driven mainly by host factors and admission severity. Detected NA/PA mutations were not robustly associated with severe outcomes, while high-level resistance could not be assessed; PA-F105L-LOS association requires phenotypic and external validation.