2. Academic Validation
  3. Emergence of the novel PA-D27G mutation conferring reduced baloxavir susceptibility in influenza A viruses circulating in China, 2018-2025

Emergence of the novel PA-D27G mutation conferring reduced baloxavir susceptibility in influenza A viruses circulating in China, 2018-2025

  • Emerg Microbes Infect. 2026 Dec;15(1):2620222. doi: 10.1080/22221751.2026.2620222.
Binhuang Sun 1,  Yulei Sun 1 2,  Hongyu Wang 1,  Xiaolu Tang 3,  Wanggang Tang 4,  Yabo Mi 2,  Zhouying Shen 1,  Quanlin Xue 1,  Yinying Lu 2,  Xiaoyu Zhao 2,  Jingwen Ai 1,  Jian Lu 3 5,  Wenhong Zhang 1 2
Affiliations

Affiliations

  • 1 Department of Infectious Diseases, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.
  • 2 Shanghai Sci-Tech Inno Center for Infection & Immunity, Institute of Infection and Health, Fudan University, Shanghai, People's Republic of China.
  • 3 State Key Laboratory of Gene Function and Modulation Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, People's Republic of China.
  • 4 Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis & Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment, School of Laboratory Medicine, Bengbu Medical University, Bengbu, People's Republic of China.
  • 5 Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, 100871, People's Republic of China.
PMID: 41555529 DOI: 10.1080/22221751.2026.2620222
Abstract

Seasonal influenza A viruses evolve rapidly, yet the emergence and molecular basis of resistance to the polymerase acidic (PA) inhibitor baloxavir marboxil (BXM), which is widely used in China, remain elusive. To address this, 3938 PA gene sequences were collected from influenza patients across mainland China between 2018 and 2025, from the national surveillance network and GISAID. By screening post-market mutations in the N-terminal domain of PA (PAN) that appeared in at least two samples and at a frequency below 50%, twenty-five single-point mutations were identified and additionally six linked mutations potentially associated with drug pressure. The impact of these mutations on BXM sensitivity was subsequently evaluated. Our analysis revealed the emergence of known mutations associated with reduced BXM sensitivity, including L28P, K34R, E198 K, although their prevalence remained low (2/3850, 0.05%). Notably, we identified a novel substitution, D27G, which conferred an approximately 12.4-fold reduction in BXM susceptibility compared with the wild-type virus and exhibited higher replication fitness than the canonical resistance mutation I38T, as demonstrated in human airway organoids. Molecular dynamics simulations further indicated that PA-D27G attenuates the interaction between PA and baloxavir acid, the active form of BXM. Epidemiological analysis showed that D27G mutation remained rare, being detected in four isolates (4/1247, 0.32%) in mainland China, and at a sporadic prevalence (<0.1%, 9/53132) across global isolates. In conclusion, these results demonstrate the early emergence of BXM-associated resistance in China and identify PA-D27G as a resistance-associated mutation with preserved viral fitness, underscoring the importance of continued genomic and epidemiologic surveillance.

Keywords

Seasonal influenza; baloxavir marboxil; drug resistance; epidemiology; human airway organoids.

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