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Volume 30, Number 9—September 2024
Dispatch
Cocirculation of Genetically Distinct Highly Pathogenic Avian Influenza H5N5 and H5N1 Viruses in Crows, Hokkaido, Japan
, Isabella Monne, Kei Nabeshima, Saki Sakuma, Asuka Kumagai, Shunya Okamura, Kosuke Soda, Hiroshi Ito, Mana Esaki, Kosuke Okuya, Makoto Ozawa, Toshiyo Yabuta, Hiroki Takakuwa, Linh Bao Nguyen, Norikazu Isoda, Kohtaro Miyazawa, Manabu Onuma, and Yoshihiro Sakoda
Table 2
BLAST search results of H5N5 HPAIVs isolated in Japan in winter 2023–24 in study of cocirculation of genetically distinct H5N5 and H5N1 HPAIVs in crows, Hokkaido, Japan*
| Virus name | Gene | Most homologous strain | Homology, % | Accession no. |
|---|---|---|---|---|
| A/large-billed crow/Hokkaido/B073/2024 (H5N5)† |
PB2 | A/Common eider/Iceland/2023AI08561/2023 (H5N5) | 99.7 | EPI2791002 |
| PB1 | A/Common eider/ Iceland/2023AI08561/2023 (H5N5) | 99.8 | EPI2791003 | |
| PA | A/Common eider/ Iceland/2023AI08561/2023 (H5N5) | 99.7 | EPI2791001 | |
| HA | A/Common gull/England/129428/2023 (H5N5) | 99.8 | EPI2815885 | |
| NP | A/Herring gull/England/404384/2023 (H5N5) | 99.9 | EPI2815894 | |
| NA | A/Herring gull/England/404384/2023 (H5N5) | 99.5 | EPI2815900 | |
| M | A/Herring gull/England/404384/2023 (H5N5) | 99.9 | EPI2815896 | |
| NS |
A/Herring gull/England/404384/2023 (H5N5) |
99.9 |
EPI2815895 |
|
| A/peregrine falcon/Kumamoto/4301C001/2024 (H5N5)‡ | PB2 | A/large-billed crow/Hokkaido/20231207001/2023 (H5N1) | 99.9 | EPI2898966 |
| PB1 | A/large-billed crow/Hokkaido/20231207001/2023 (H5N1) | 99.9 | EPI2898967 | |
| PA | A/large-billed crow/Hokkaido/0111Q100/2023 (H5N1) | 99.8 | EPI2841124 | |
| HA | A/large-billed crow/Hokkaido/20231207001/2023 (H5N1) | 99.9 | EPI2898969 | |
| NP | A/large-billed crow/Hokkaido/0112Q104/2023 (H5N1) | 99.7 | EPI2815894 | |
| NA | A/Duck/Hokkaido/W24/ 2020 (H6N5) | 99.1 | EPI1896526 | |
| M | A/large-billed crow/Hokkaido/20231207001/2023 (H5N1) | 100 | EPI2815896 | |
| NS | A/large-billed crow/Hokkaido/20231207001/2023 (H5N1) | 99.9 | EPI2898973 |
*Gene segment sequences of 2 H5N5 HPAIVs were compared with those of other H5 virus sequences by using BLAST (https://blast.ncbi.nlm.nih.gov). Accession numbers are from GISAID (https://www.gisaid.org). HA, hemagglutinin; HPAIV, highly pathogenic avian influenza virus; M, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, nonstructural protein; PA, polymerase acidic; PB1, polymerase basic 1; PB2, polymerase basic 2. †H5N5 HPAIV isolated in Hokkaido in winter 2023–24. ‡H5N5 HPAIV isolated in Kumamoto Prefecture in winter 2023–24.