Seasonal Dynamics and Genotype Turnover of H5N1 High-Pathogenicity Avian Influenza Viruses in Wild Birds and Crane Roost Water in the Izumi Plain, Japan, 2024/25

Clade 2.3.4.4b H5N1 high-pathogenicity avian influenza viruses (HPAIVs) continue to circulate extensively in wild-bird populations, yet temporal changes in genetically distinct viral populations within a single overwintering season remain poorly understood. We investigated H5N1 HPAIV dynamics in the Izumi Plain, Japan, during the 2024/25 winter season by combining virological surveillance of dead or debilitated wild birds with longitudinal virus isolation from crane roost water. Tracheal and cloacal swabs from 111 wild birds and 256 water samples collected weekly from two crane roosting sites were examined, and isolated viruses were characterized by phylogenetic and whole-genome genotype analyses. Among 103 cranes tested, 64 were positive for H5N1 HPAIV, and viruses were isolated from 58 birds. H5N1 HPAIVs were also isolated from two Eurasian Wigeons and one Northern Goshawk. All H5N1 HPAIV isolates belonged to the G2c or G2d subgroup within clade 2.3.4.4b. Both subgroups circulated in wild birds and the roost environment during 2024, whereas only G2c viruses were detected after January 2025. Whole-genome analysis classified the H5N1 HPAIV isolates into six genotypes and revealed complete replacement of the circulating genotypes around the turn of the year; all isolates obtained in 2025 belonged to genotype H5N1-VI, which had not been detected in 2024. H5N1-VI was characterized by a distinct PB1 gene segment that was not detected among low-pathogenicity AIVs isolated from the same roost environment. These findings demonstrate substantial within-season changes in H5N1 HPAIV populations at a major wild-bird overwintering site and highlight the value of integrating environmental and wild-bird surveillance with whole-genome analysis to characterize temporal changes and genotype turnover throughout the wintering season.