National Institute of Animal Health, NARO

Characteristics of the H5N1 subtype HPAIV detected from crows in Hokkaido in October 2023

The National Agriculture and Food Research Organization (NARO) has conducted whole-genome sequencing of a high pathogenicity avian influenza virus (HPAIV) isolated from a dead large-billed crow in Bibai city, Hokkaido prefecture on October 4, 2023. It has been revealed that this virus is classified into the same genotype as H5N1 subtype HPAIV detected in Japan during the 2021/2022 season (fall 2021 to spring 2022) and 2022/2023 season (fall 2022 to spring 2023). Since 2004, this is the first time that same genotype virus has been detected in Japan for three consecutive seasons. From the fact that HPAIV has already been confirmed in wild birds in Japan, we need to be more vigilant against the invasion of the virus into the poultry facilities.


A dead large-billed crow was collected in Bibai city, Hokkaido prefecture on October 4, 2023 in the surveillance of high pathogenicity avian influenza (HPAI) in wild birds conducted by the Ministry of the Environment in collaboration with prefectures in Japan. After the confirmation of the influenza A virus by the commercial rapid test, genetic analysis was performed at the National Institute for Environmental Studies, and they detected H5N1 subtype HPAIV. This is the first domestic case of HPAI in wild birds this season.

NARO conducted virus isolation from specimens derived from the large-billed crow and whole genome sequencing of this isolate (designated as Hokkaido strain). A phylogenetic tree analysis was performed on the eight gene segments, and the genotype was determined based on the combination of gene segments. From the results, it was revealed that the isolated virus strain (Hokkaido strain) was classified as genotype G2d-0 (21E-0 in previous reports), which was detected in Japan in the 2021/2022 and 2022/2023 seasons ( This is the first time since 2004 that same genotype virus has been confirmed in Japan for three consecutive seasons.

In addition, the Hokkaido strain does not contain any amino acid mutations which confer resistance against neuraminidase inhibitors and viral RNA polymerase inhibitors. Amino acid mutations which increase the infectivity in mammals were not confirmed. Therefore, it is estimated that there is a low possibility of human infection.

Migratory birds such as ducks have been arriving in Bibai city, Hokkaido from early September. Since the large-billed crow in which the virus was detected is a scavenger (an omnivorous animal that also eats dead animals), it was thought that it may have been infected by consuming a carcass infected with HPAIV. In the future, an increased alert is required against the invasion of the virus into the poultry facilities, as HPAIV has been confirmed already in wild birds in Japan.

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