A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus

Abstract

Using phylogenetic analysis on newly available sequences, we characterize A/chicken/Jiangsu/RD5/2013(H10N9) as currently closest precursor strain for the NA segment in the novel avian-origin H7N9 virus responsible for an outbreak in China. We also show that the internal segments of this precursor strain are closely related to those of the presumed precursor for the HA segment, A/duck/Zhejiang/12/2011(H7N3), which indicates that the sources of both HA and NA donors for the reassortant virus are of regional and not migratory-bird origin and highlights the role of chicken already in the early reassortment events.

Figure 1

A new JS5-like(H10N9) precursor is the closest NA segment relative to the 2013 H7N9 and its internal genes are closely related to the HA donor ZJ12-like(H7N3). (A) Maximum likelihood phylogenetic tree of NA gene segments shows the NA from the novel avian-origin H7N9 virus (green) is more closely related to JS5-like (H10N9, red) than KO14-like (H7N9, blue) and precursors proposed by Lam et al. (pink). Methods: The H7N9 outbreak sequences were downloaded from GISAID’s EpiFlu™ database on June 13th 2013 (detailed acknowledgment in additional file 3) and complemented with best BLAST hits from Genbank as well as selected older representative strains as outgroup. The sequences were aligned with MAFFT using the L-INS-I parameters, the alignment was checked in Jalview and a nonredundant subset with less than 100% identity was retained. The phylogenetic tree was generated in PhyML with a gamma-distributed HKY85 substitution model. Positions with gaps and missing data were completely deleted, and 1000-replicate bootstrapping was performed; an average of these replicates is shown. (B), (C) Phylogenetic analysis of internal segments amongst H7N9 strains and other closely related strains shows close identity between the ZJ12-like(H7N3, dark blue) HA donor and JS5-like(H10N9, red) NA donor. Maximum-likelihood trees using nucleotide sequences of (B) NP and (C) PB2 gene segments were generated as described before. Reassortant H7N9 strains (green), presumed BJ16-like internal segment donor (purple), previously postulated KO14-like (H7N9) NA donor (blue), newly proposed N9 relative from Lam et al. (pink) and internal gene relatives from Wu et al. (dark red) are also indicated. (D) The NA gene segment of the reassortant H7N9 virus derives from JS5-like (H10N9, red), the HA gene segment from ZJ12-like (H7N3, blue) and the internal segments derive from BJ16-like or ZJ04-like (H9N2, orange) strains.