National Institute of Animal Health, NARO

Genetic diversity of domestic highly pathogenic avian influenza virus of this season

The National Institute of Animal Health, NARO (NIAH) has decoded the entire genome of 57 strains of H5N8 subtype highly pathogenic avian influenza virus (HPAIV) of the specimens obtained from domestic poultry farm and wild birds from November 5, 2020 to February 16, 2021.The combination of eight gene segments carried by these viruses was analyzed. From the analysis it was found that five virus genotypes have invaded the country and four virus genotypes are involved in the outbreak in poultry farm.


The first H5N8 HPAI Virus of the season was observed in the feces of wild birds in Hokkaido on October 24, 2020. On November 5, 2020, an outbreak of H5N8 highly pathogenic avian influenza virus was confirmed in a domestic poultry farm. Until February 28, 2021, HPAIV outbreaks at Poultry farms accounts to 51 cases in 17 prefectures from Ibaraki prefecture to Kagoshima prefecture. For wild birds, 56 cases in 18 prefectures from Hokkaido to Kagoshima prefecture have been reported.

In order to estimate the association of H5N8 subtype HPAIV obtained from poultry farm and wild birds and the pathway of virus invasion and their outspread, researchers from NIAH has decoded the entire genome of 57 strains obtained from 49 specimens in poultry farm nationwide (November 5, 2020 to February 11, 2021) and 8 specimens in wild bird from the Kantoukoushin'etsu and Hokuriku regions (November 5, 2020 to February 16, 2021).

Phylogenetic tree analysis was performed for each segment of the virus which was decoded this time, as the influenza A virus is composed of eight gene segments (PB2, PB1, PA, HA, NP, NA, MP and NS gene segments). In the HA and NA gene segments which determines the viral subtypes, they observed the virus which was the source of two strains namely H5N8 subtype HPAIV strain that was prevalent in Europe in 2019-2020 (European lineage HPAIV strains Winter 19-20) and H5N8 subtype HPAIV strain reported in Russia and Europe in 2020-2021 (European lineage HPAIV strain Autumn 20). Among them, In European lineage HPAIV strain Winter 19-20, four types of PB2, PB1, PA and NP gene segments other than HA and NA were found to be originated from HPAI Virus from wild birds. It was clarified that a total of 5 different combinations (genotypes) of viruses invaded the country depending on the combination of each segment. No resistance mutations to the antiviral neuraminidase inhibitors and viral RNA polymerase inhibitors were found in the putative amino acid sequences of the five virus genotypes. Also, no known amino acid mutations have been found to increase infectivity to mammals.

In the future, experimental infections will be carried out for the five virus genotypes, in order to investigate the lethality of poultry and the viral replication in the body.

Reference Information

Figure 1. Genotype of this season's H5N8 subtype highly pathogenic avian influenza virus
based on 8-segment gene Phylogenetic Tree Analysis

It is classified into two strains according to the gene segment (HA and NA) that determines the subtype. It is classified into a total of 5 types of genotypes by combining other gene segments.

Figure 2. Prefectural distribution map of H5N8 subtype HPAIV genotypes derived from
domestic poultry and some local wild birds this season

Outbreaks in poultry were observed in Ibaraki and Kagoshima prefectures, and four genotype viruses (1), (2), (3) and (5) have been isolated. In wild birds, viruses of genotypes 1, 3, 4 and 5 have been isolated.