This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Dalby AR, Iqbal M. (2014) A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 Influenza Hemagglutinin. PeerJ PrePrints2:e499v1https://doi.org/10.7287/peerj.preprints.499v1
A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species.
The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment.
The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
This manuscript is under review at PeerJ. This is a version of the paper which is a response to reviewers comments.
Expanded Phylogenetic Tree
The Expanded Phylogenetic Tree. In this figure all of the clades have been expanded to show the leaf nodes.
Model test results for the evaluation of the different amino acid substitution models used to build the phylogenetic trees
Model test results for the evaluation of the different amino acid substitution models used to build the phylogenetic trees. Results are evaluated using Bayesian Information Criteria, Akaike's Information Criteria and Log Likelihood.
Model test results for the evaluation of the different nucleotide substitution models used to build the phylogenetic trees
Model test results for the evaluation of the different nucleotide substitution models used to build the phylogenetic trees. Results are evaluated using Bayesian Information Criteria, Akaike's Information Criteria and Log Likelihood.
This contains the raw protein and nucleotide sequence files in fasta format
There are two directories one for the protein sequences and a second for the nucleotide sequences. There are also two MEGA files that include the nucleotide alignment (.mas file) and the phylogenetic trees (.mts file).
"Following" is like subscribing to any updates related to a preprint.
These updates will appear in your home dashboard each time you visit PeerJ.
You can also choose to receive updates via daily or weekly email digests.
If you are following multiple preprints then we will send you
no more than one email per day or week based on your preferences.
Note: You are now also subscribed to the subject areas of this preprint
and will receive updates in the daily or weekly email digests if turned on.
You can add specific subject areas through your profile settings.