BRIEF RESEARCH REPORT article
Front. Cell. Infect. Microbiol.
Sec. Veterinary and Zoonotic Infection
This article is part of the Research TopicSequencing Technologies in Advancing Veterinary and Zoonotic Infection ResearchView all 9 articles
Early Detection and Genetic Characterization of Clade 2.3.4.4b H5N1 and H5N9 Highly Pathogenic Avian Influenza Viruses at the Onset of Fall Migration in Wild Birds during October 2025 in South Korea
Provisionally accepted
- 1National Institute of Wildlife of Disease Control and Prevention, Gwangju, Republic of Korea
- 2Konkuk University, Seoul, Republic of Korea
- 3Wildlife Health Laboratory, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
- 4Avian disease laboratory, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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Highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4b continue to diversify through reassortment with co-circulating low-pathogenic avian influenza (LPAI) viruses and are repeatedly introduced into South Korea via migratory flyways. During national wild bird surveillance in October 2025, two HPAI viruses of different subtypes, H5N1 and H5N9, were detected in Common teals in the southwestern Korea. Whole-genome sequencing confirmed both isolates as clade 2.3.4.4b viruses belonging to the G2c sub-lineage. Phylogenetic analysis showed that the H5N1 virus possessed a genomic backbone related to the 22G4 genotype circulating in Korea during the 2022–2023 season, incorporating a PB1 segment derived from LPAI viruses. The H5N9 virus represented a distinct reassortant carrying an NA gene closely related to H11N9 LPAI viruses and internal segments associated with KorD and KorC genotypes prevalent in the same season. Bayesian time-scaled analysis indicated that both isolates originated from an East Asian H5Nx lineage with a common ancestor around 2019, and that the H5N1 virus diverged from a closely related Chinese strain in late 2023. Both viruses harbored multiple mammalian-adaptation markers, including substitutions commonly detected in recent East Asian HPAI strains. These findings demonstrate ongoing inter-lineage reassortment between regional HPAI and LPAI gene pools, emphasizing the continued role of migratory waterfowl in introducing emerging variants into Korea. The early-season detection of genetically distinct reassortants highlights the importance of sustained wild bird surveillance, rapid genomic characterization, and international data sharing to track the evolution and spread of newly emerging HPAI lineages.
Keywords: clade 2.3.4.4b, Eurasian Teal, H5N1, H5N9, highly pathogenicity avian influenza, phylogenetic analysis, South Korea
Received: 27 Nov 2025; Accepted: 02 Jan 2026.
Copyright: © 2026 Si, Lee, Lee, Kim, Jeong, Lee and Lee. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dong-Hun Lee
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