National Agriculture and Food Research Organization (NARO) has conducted genetic analysis on 60 cases of high pathogenicity avian influenza virus (HPAIV) identified in domestic poultry facilities from October 28, 2022 to January 17, 2023. From the analysis result it was revealed that in 2022 season, there were three groups classified by the characteristics of the hemagglutinin (HA) gene invaded Japan at the same period and in a wide range from the earliest time so far. Two of these groups are closely related to groups detected in Japan last season, and one newly detected group is closely related to viruses isolated in West Siberia and Central China in 2021. Since this season has the highest number of outbreaks ever it is necessary to continue to monitor the trend of the HPAIV epidemic and be vigilant against the invasion of the virus into Japan and farms.
Overview
On October 28, 2022, the earliest outbreak of high pathogenicity avian influenza (HPAI) since 2004 occurred at poultry farms in Okayama Prefecture and Hokkaido. H5N1 subtype high pathogenicity avian influenza virus (HPAIV) was isolated from dead chickens, followed by 60 outbreaks of H5 subtype HPAI by January 17, 2023. Of the 60 cases, 59 cases were caused by H5N1 subtype HPAIV and 1 case was caused by H5N2 subtype HPAIV, which is the highest number of outbreaks ever.
Whole genome of HPAIV isolated from outbreaks 1 to 59 (H5N1 subtype) and 60 (H5N2 subtype) were sequenced and phylogenetic tree analysis for the hemagglutinin (HA) gene segment was conducted.
The phylogenetic tree showed that it is closely related to the two groups "2020-2021 Winter European HPAIV (20E)" and "2021-2022 European HPAIV (21E)" detected in Japan in the 2021 season. In addition, a virus closely related to "2021 West Siberian and Chinese isolated HPAIV (21RC)" was newly detected. It was revealed that three groups of viruses such as 20E, 21E and 21RC had invaded Japan during the same period from the beginning of the season. HA of H5N2 subtype HPAIV was classified into 21E group, and it was revealed that all gene segments are closely related to H5N2 subtype HPAIV detected from jungle crow in Hokkaido on November 28, 2022. 172 cases of H5 subtype HPAIV were also detected in wild birds or environmental samples from September 25,2022 to January 20,2023. H5 subtype HPAIV of 20E, 21E and 21RC groups has been detected in few analyzed samples, as well as in the poultry. As in the 2021 season, virus groups detected during the previous season's outbreaks were recognized in the 2022 season. However, it was the first time that multiple groups seen in previous seasons were detected. Since HPAI and HPAIV were detected at the same time as the migration season of migratory birds, it was thought that HPAIV which was transported at the end of the 2021 season when the migratory birds returned to the north might have entered Siberia, a breeding ground, and maintained among wild birds. Then the virus might be brought back to Japan by the migratory birds which arrived to overwinter.
By analyzing the HA gene groups of viruses isolated in poultry and their association with the time and place of occurrence, it was evident that from the beginning of the outbreak to January 2023, outbreaks due to 3 groups of viruses were recognized without any temporal or geographical bias. Multiple groups of viruses were involved in poultry outbreaks in Aomori, Niigata, Ibaraki, Okayama, Fukuoka and Kagoshima prefectures.
From the analysis of outbreak information and detected viruses in poultry and wild birds in the 2022 season, it was revealed that at least three viruses with different genetic backgrounds have been identified as the earliest to enter the country, causing the largest number of widespread outbreaks. Therefore, we need to be even more vigilant against the invasion of the virus into farms in the future.
In the deduced amino acid sequences of virus strains isolated from 59 cases, no mutations related to resistance to existing representative antiviral drugs or virus replication in mammals were observed. In addition, the deduced amino acid sequence of the virus strain isolated from one emu case had mutations that facilitated replication in mammals, like those previously reported in emu isolates. No other mutations were observed in the deduced amino acid sequence, so the virus is unlikely to directly infect humans.
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