Five distinct reassortants of H5N6 highly pathogenic avian influenza A viruses affected Japan during the winter of 2016–2017

Abstract

To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016-2017 and 117 AIV/HPAIVs isolated in Japan and Russia. Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that period. Japanese H5N6 isolates shared a common genetic ancestor in 6 of 8 genomic segments, and the PA and NS genes demonstrated 4 and 2 genetic origins, respectively. Six gene segments originated from a putative ancestral clade 2.3.4.4 H5N6 virus that was a possible genetic reassortant among Chinese clade 2.3.4.4 H5N6 HPAIVs. In addition, 2 NS clusters and a PA cluster in Japanese H5N6 HPAIVs originated from Chinese HPAIVs, whereas 3 distinct AIV-derived PA clusters were evident. These results suggest that migratory birds were important in the spread and genetic diversification of clade 2.3.4.4 H5 HPAIVs.

Phylogenetic variations of highly pathogenic H5N6 avian influenza viruses isolated from wild birds in the Izumi plain, Japan, during the 2016–17 winter season

“…In the constructed phylogenetic trees based on the H5 HA (Supporting information Figure S1A), N6 NA (Supporting information Figure S1B), NP (Supporting information Figure S2A), and M (Supporting information Figure S2B) genes, the 33 H5N6 HPAIV isolates formed a single cluster with the other contemporary H5N6 HPAIV isolates. Consistent with previous findings (Hiono et al., ; Takemae et al., ), our results suggested no phylogenetic variations in the four gene segments of all H5N6 HPAIVs isolated globally during the 2016–2017 winter season.…”

“…By contrast, we identified previously unreported phylogenetic variations in the PB2, PB1, PA, and NS gene segments (Figure a‐d). The NS genes of previously reported H5N6 HPAIV isolates during the 2016–2017 winter season were classified into two phylogenetic groups, namely, NS‐I and NS‐II (Takemae et al., ). The phylogenetic tree based on the NS genes (Figure d) clustered the 33 H5N6 HPAIV isolates into two phylogenetic groups; however, one of the phylogenetic groups (designated NS‐III in Figure d) formed a single cluster that was separated from those of the other contemporary H5N6 HPAIV isolates.…”

“…The PA genes of previously reported H5N6 HPAIV isolates during the 2016–2017 winter season were divided into four phylogenetic groups, namely, PA‐I, ‐II, ‐III, and ‐IV (Takemae et al., ). As described above, 11 of the 33 H5N6 HPAIV isolates were clustered into the two additional phylogenetic groups (PA‐V and ‐VI in Figure c).…”

“…Previously reported H5N6 HPAIV isolates during the 2016–2017 winter season were divided into six genotypes C1–C6, based on four and two phylogenetic variations in the PA and NS gene segments respectively (Figure c,d) (Hiono et al., ; Lee et al., ; Takemae et al., ). Phylogenetic analyses identified variations in the PB2 (Figure a) and PB1 (Figure b) gene segments and two and one additional phylogenetic variations in the PA (Figure c) and NS (Figure d) gene segments, respectively, among H5N6 HPAIV isolates during the same season.…”

“…Genome sequencing of the early Korean isolates revealed that the H5N6 HPAIVs can be classified into five genotypes (C1–C5) that harboured four (PA‐I to ‐IV) and two (NS‐I and ‐II) phylogenetic variations in the PA and NS gene segments, respectively (Lee et al., ). Subsequently, all H5N6 HPAIVs previously isolated in Japan, including two early isolates from the Izumi plain, were classified into the four known genotypes (C1, C2, C4, and C5) (Hiono et al., ; Okamatsu et al., ; Takemae et al., ), except for one isolate A/chicken/Miyazaki/2‐1T/2017(H5N6) whose PA gene segment was phylogenetically distinct from those of the remaining contemporary H5N6 HPAIV isolates. Therefore, A/chicken/Miyazaki/2‐1T/2017(H5N6) was classified under the genotype C6 (Takemae et al., ).…”