Last piece of the story - my appeal letter

Dear Editor, 

I would like to submit the article “The multiple origins of the H5N8 avian influenza sub-type”. This paper describes the multiple reassortment events that have produced the H5N8 avian influenza sub-type. The current phylogenetic tree for the H5N8 sequences is calculated and this does not exhibit any unusual features. There seem to be clades in the Far East and North America.

What this does phylogenetic tree does not show is that the appartently homogeneous North American clade is actually made up of multiple distinct re-assortment events. These are usually just single isolated sequences, and this suggests that while the sub-type is present other H5 and N8 containing sub-types dominate and this is a rare reassortment that rapidly becomes extinct. 

By carrying out a phylogenetic analysis of all the H5 segments from all H5 containing subtypes it is clear that the H5 is evolving in different subtypes between reassortment events that create H5N8 and the same is true for the N8 segments. This is the novel aspect of the research and shows that there are many re-assortment events that need to be accounted for but which are undetectable in the H5N8 sequences only trees. By not taking these re-assortments the the subsequent sequence evolution in other H5 or N8 containing sub-types into account we cannot correctly calculate the H5N8 phylogeny. Both the H5N8 phylogenies have been calculated using the same method (maximum likelihood) and the same evolutionary model (GTR with gamma correction). However the phylogenies for H5 and N8 were computed using FastTree rather than in Mega or PhyML because there are over 4000 H5 taxa and so they cannot be computed with bootstraps. However despite the lack of bootstrap values both the H5 and N8 phylogenies exhibit the same patterns of isolated re-assortment events, showing that the trees are a good representation of the true phylogenetic relationship.

The usual failure to propagate of H5N8 re-assortments is very important in the context of the current outbreak because this is the first time that the H5N8 subtype has persisted over such a long period of time. This has allowed the virus to spread globally through bird migration spreading the pathogenic Chinese H5 variant.

Thank you for your consideration.