Rapid reassortment of internal genes in avian influenza A(H7N9) virus.

TO THE EDITOR—H7N9 is a novel avian virus recently first reported from Shanghai in China. Very recently an isolate from Taiwan was also reported [1]. H7N9 is able to infect humans and has caused many fatal cases [2, 3]. Determining the origin and evolution of these disease-causing viruses is important for surveillance and prevention of the influenza epidemics. With more and more reported pathogenic H7N9 isolates reported, it is important to reexamine whether these disease-causing H7N9 isolates all came from the same common ancestor and whether they have undergone further reassortments. Previous studies indicated that the 6 H7N9 internal genes were from a single avian H9N2 strain [3] or from a reassortment of 2 separate H9N2 strains: the NS gene was from an H9N2 strain in the Jiangsu area, whereas the other 5 genes, M, NP, PA, PB1, and PB2, were from the other H9N2 strain in the Zhejiang area [4]. Our results are consistent with the previous results regarding the origins of HA, NA, and NS; however, we found that the remaining 5 internal genes (M, NP, PA, PB1, and PB2) appeared to come from multiple sources as they were grouped into 2 or 3 clusters in the phylogenetic trees (Figure 1). However, for M, PA, PB1, and PB2, each has a cluster together with the A/brambling/Beijing/16/2012, suggesting that they may have originated from the brambling, and each of them has another cluster due to rapid assortments. Based on these different clusters, the current H7N9 isolates can be grouped into 9 lineages or genotypes (Figure 1I). The phylogenetic tree of the H7N9 M gene has 2 separate clusters, with Shanghai/Patient4, Hangzhou/3, Shanghai/ Patient2, Shanghai/Patient5, and Taiwan/ 1 in one cluster closing the A/brambling/ Beijing/16/2012, and the remaining H7N9 strains forming the other cluster (Figure 1D). This observation indicates that the M genes in these 2 clusters may have originated from 2 different H9N2 strains. We also calculated the nucleotide substitution rate for each gene of H7N9. The nucleotide substitution rates for the 3 single-origin genes HA, NA, and NS (approximately 0.0068) are lower than the