Background: Clinical data on patients infected with influenza B Victoria (BV) after the approval of baloxavir is lacking.

Methods: This observational study of the Japanese 2023-2024 influenza season analyzed data from 25 outpatients with A(H1N1)pdm09, 36 with A(H3N2), and 65 with BV. Viral samples were collected before and after administering an antiviral (70 patients received baloxavir and 56 received a neuraminidase inhibitor), on days 1, 5, and 10. Isolated viruses after culturing were amplified using RT-PCR and sequenced to detect mutations of concern, including acidic protein (PA)-amino acid (AA) E23X/I38X for influenza A and M34X/I38X for BV. Fever and symptoms were tracked via self-reporting diaries.

Results: No PA-AA-substituted virus was detected from 126 pre-treatment samples. In the baloxavir cohort, one (7.1%, 1/14) PA I38F-substituted A(H1N1)pdm09 and two (11.1%, 2/18) PA I38T-substituted A(H3N2) viruses were isolated on day 5 but not on day 10. No (0%, 0/37) PA-AA-substituted BV was detected on day 5 or after. The virus isolation rate on day 5 was higher among patients with BV than with influenza A in both baloxavir (35.1% vs. 14.3% for A(H1N1)pdm09 and 16.7% for A(H3N2)) and oseltamivir-treated patients (44.4% vs. 0% for A(H1N1)pdm09 and 33.3% for A(H3N2)). Patients with PA-AA-substituted influenza A after baloxavir administration did not have longer fever duration than those without virus isolation or with wild-type virus on day 5, for both A(H1N1)pdm09 and A(H3N2).

Conclusions: Baloxavir-resistant variants were not detected in influenza BV before treatment, as with A. The emergence of PA-AA-substituted influenza A after baloxavir administration was temporal and did not cause prolonged symptoms. No baloxavir-resistant BV variants were observed after baloxavir administration.