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The objective of this study was to estimate the efficacy of the neuraminidase (NA) inhibitors (NAIs) oseltamivir and zanamivir for decreasing viral load and to investigate whether NAI treatment decreases viral susceptibility to NAIs over time in children with influenza B virus infection.Of 27 patients with influenza B virus infection, 8 and 9 were treated with oseltamivir and zanamivir, respectively, whereas 10 received no NAI. Nasal aspiration samples, collected every morning until negative antigen results in 2 consecutive samples were observed, were subjected to viral load measurements by quantitative real-time reverse transcription polymerase chain reaction and viral susceptibility to NAI by NA inhibition assays.Viral load decreased in both the oseltamivir and zanamivir groups by day 2 but increased in the no-NAI treatment group. Viral load in the oseltamivir and zanamivir groups on day 5 was 2.6% and 9.2% of that on day 0, respectively, whereas it was 26.4% in the no-NAI treatment group. Mean 50% inhibitory concentration (IC50) values of oseltamivir and zanamivir in the no-NAI treatment group were 5.0–6.6 and 1.3–1.8 nM, respectively. Mean IC50 values of oseltamivir and zanamivir in patients treated with oseltamivir and zanamivir were 3.9–8.8 and 1.3–1.8 nM, respectively. No major decrease in viral susceptibility to NAIs was observed during or after NAI treatment.NAI treatment was effective for inhibiting viral replication during the early days of illness and did not decrease viral susceptibility to NAIs in patients with influenza B virus infection.