Reassortment history leading to human H7N9 outbreak
We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiFlu™ Database on which this analysis is based. A list of the sequences, their submitting labs and GISAID links is provided on this page.
To look at the reassortment history of the outbreak viruses it was necessary to compile a dataset that contained exactly the same strains in the alignments for each segment. To do this I used GISAID's BLAST feature to find the closest 250 sequences for each segment of A/Shanghai/1/2013 but downloaded all 8 segment sequences (if available) for the matched isolates. I then used a script to separate out the gene segments into different files and remove duplicates. A bit of clean up to remove very short sequences and certain problem sequences gave 8 alignments of about 1200-1400 sequences each.
The alignments were done using MAFFT in Geneious and are not manually adjusted because of their size.
By loading all 8 trees into FigTree, we can colour certain sequences names in one tree (for example, the closest relatives to the human H7N9) and see where they appear in each of the other trees.
In blue are the new human cases. In green are the nearest avian isolates for this gene (segment 4, HA). In pink are the nearest isolates in the NA gene (segment 6).
Inset of tree for segment 6, NA showing human strains in blue and the closest relatives in pink.
Overview of the full segment 4, HA tree. 2 HA subtypes are highlighted due to their involvement with the human outbreak origins. In green is the H7 subtype which has the close avian relatives of the human viruses for HA (H7N3 viruses) and also the closest relatives in the NA gene tree (H7N9). In red is the N2 subtype which contains the H9N2 viruses which are the closest relatives of the human clade for the internal genes (Segments 1, 2, 3, 5, 7 & 8).
Overview of the full NA tree. 3 NA subtypes are highlighted due to their involvement with the human outbreak origins. In pink is the N9 subtype which has the close avian relatives of the human viruses (see inset in figure above). In green is the N3 subtype which contains the closest relatives of the human virus for the HA gene segment (these are the H7N3 viruses highlighted in green in the inset figure of the HA tree). Finally in red is the N2 subtype which contains the H9N2 viruses which are the closest relatives of the human clade for the internal genes (Segments 1, 2, 3, 5, 7 & 8).
In segment 3, PA, the human clade (blue) is nested within a predominantly Chinese duck and chicken clade of H9N2 viruses with A/brambling/Beijing/16/2012 being the closest relative (a brambling is a wild bird).