Genetic diversity of H5N1 and H5N2 high pathogenicity avian influenza viruses isolated from poultry in Japan during the winter of 2022-2023

Abstract

High pathogenicity avian influenza viruses (HPAIVs) of the H5N1 and H5N2 subtypes were responsible for 84 HPAI outbreaks on poultry premises in Japan during October 2022-April 2023. The number of outbreaks during the winter of 2022-2023 is the largest ever reported in Japan. In this study, we performed phylogenetic analyses using the full genetic sequences of HPAIVs isolated in Japan during 2022-2023 and those obtained from a public database to identify their genetic origin. Based on the hemagglutinin genes, these HPAIVs were classified into the G2 group of clade 2.3.4.4b, whose ancestors were H5 HPAIVs that circulated in Europe in late 2020, and were then further divided into three subgroups (G2b, G2d, and G2c). Approximately one-third of these viruses were classified into the G2b and G2d groups, which also included H5N1 HPAIVs detected in Japan during 2021-2022. In contrast, the remaining two-thirds were classified into the G2c group, which originated from H5N1 HPAIVs isolated in Asian countries and Russia during the winter of 2021-2022. Unlike the G2b and G2d viruses, the G2c viruses were first detected in Japan in the fall of 2022. Importantly, G2c viruses caused the largest number of outbreaks throughout Japan over the longest period during the season. Phylogenetic analyses using eight segment genes revealed that G2b, G2d, and G2c viruses were divided into 2, 4, and 11 genotypes, respectively, because they have various internal genes closely related to those of avian influenza viruses detected in wild birds in recent years in Asia, Russia, and North America, respectively. These results suggest that HPAIVs were disseminated among migratory birds, which may have generated numerous reassortant viruses with various gene constellations, resulting in a considerable number of outbreaks during the winter of 2022-2023.

Keywords: H5N1; H5N2; High pathogenicity avian influenza virus; Phylogenetic analysis; Poultry; Winter of 2022–2023.

Fig. 1

Phylogenetic analysis of the G2 group HA gene segment and occurrence ratio, periods, and prefectures of outbreaks. (a) The entire phylogenetic tree of hemagglutinin (HA), including groups G2a, G2b, G2c, and G2d. (b) Pie chart showing the ratios of outbreaks caused by the three groups. (c) The numbers of outbreaks caused by the three groups from October 2022 to April 2023. Asterisks indicate the absence of outbreaks reported during the study period. (d) The prefectures in which outbreaks were caused by G2b, G2d, and G2c during the winter of 2022–2023.

Fig. 2

Phylogenetic analysis of the HA gene segment of G2b, G2d, and G2c viruses. Detailed phylogenetic trees of the hemagglutinin (HA) from G2b, G2d, and G2c are shown in (a), (b), and (c), respectively. The red and blue-colored strains are the HPAIV strains detected in Japan during the 2022–2023 and 2021–2022, respectively. The strain with the filled circle indicates the virus isolated and sequenced in this study. The numbers shown on the nodes of the phylogenetic trees are fast-global bootstrap values of >60 %.

Fig. 2

Phylogenetic analysis of the HA gene segment of G2b, G2d, and G2c viruses. Detailed phylogenetic trees of the hemagglutinin (HA) from G2b, G2d, and G2c are shown in (a), (b), and (c), respectively. The red and blue-colored strains are the HPAIV strains detected in Japan during the 2022–2023 and 2021–2022, respectively. The strain with the filled circle indicates the virus isolated and sequenced in this study. The numbers shown on the nodes of the phylogenetic trees are fast-global bootstrap values of >60 %.

Fig. 2

Phylogenetic analysis of the HA gene segment of G2b, G2d, and G2c viruses. Detailed phylogenetic trees of the hemagglutinin (HA) from G2b, G2d, and G2c are shown in (a), (b), and (c), respectively. The red and blue-colored strains are the HPAIV strains detected in Japan during the 2022–2023 and 2021–2022, respectively. The strain with the filled circle indicates the virus isolated and sequenced in this study. The numbers shown on the nodes of the phylogenetic trees are fast-global bootstrap values of >60 %.

Fig. 3

Phylogenetic analysis of the N1 and N2 subtype neuraminidase gene segments. (a) The entire phylogenetic tree of N1 neuraminidase (NA), including G2b, G2c, and G2d. (b) Detailed phylogenetic trees of the N2 NA gene. The red-colored strains are HPAIV strains detected in Japan in 2022–2023. The strain with the filled circle indicates the virus isolated and sequenced in this study. The numbers shown on the nodes of the phylogenetic trees are fast-global bootstrap values of >60 %.

Fig. 4

Occurrence and periods of outbreaks in prefectures by genotypes in groups G2b, G2d, and G2c. (a–c) Prefectures and periods of outbreaks caused by the G2b, G2d, and G2c genotypes.