A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin

Dalby, A.R. and 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. 2 e655. https://doi.org/10.7717/peerj.655

TitleA global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin
AuthorsDalby, A.R.
Iqbal, M.
Abstract

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.

KeywordsH9N2, avian influenza, hemagglutinin, phylogenetics, geography, host species
Article numbere655
JournalPeerJ
Journal citation2
Year2014
Publisher's version
Digital Object Identifier (DOI)https://doi.org/10.7717/peerj.655

Related outputs

Bacterial Adaptation to Venom in Snakes and Arachnida
Esmaeilishirazifard, Elham, Usher, Louise, Trim, Carol, Denise, Hubert, Sangal, V., Tyson, G., Barlow, Axel, Redway, Keith F, Taylor, John D, Kremyda-Vlachou, Myrto, Davies, Sam, Loftus, Teresa D, Lock, Mikaella M G, Wright, Kstir, Dalby, Andrew, Snyder, L., Wuster, Wolfgang, Trim, Steve and Moschos, S. 2022. Bacterial Adaptation to Venom in Snakes and Arachnida. Microbiology Spectrum. 10 (3) e02408-21. https://doi.org/10.1128/spectrum.02408-21

Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events
Dalby, A.R. 2016. Complete analysis of the H5 hemagglutinin and N8 neuraminidase phylogenetic trees reveals that the H5N8 subtype has been produced by multiple reassortment events. F1000Research . 5, p. 2463 2463. https://doi.org/10.12688/f1000research.9261.1

Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation
Dalby, A.R. and Shamsir, M. 2015. Molecular dynamics simulations of the temperature-induced unfolding of crambin follow the Arrhenius equation. F1000Research. 4 (589). https://doi.org/10.12688/f1000research.6831.1

The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways
Dalby, A.R. and Iqbal, M. 2015. The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways. PeerJ. 3 e934. https://doi.org/10.7717/peerj.934

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Dalby, A.R. and Bailey, I. 2014. The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma. Microarrays. 3 (4), pp. 212-225. https://doi.org/10.3390/microarrays3040212

Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level
Dalby, A.R., Emam, I. and Franke, R. 2012. Analysis of gene expression data from non-small celllung carcinoma cell lines reveals distinct sub-classesfrom those identified at the phenotype level. PLoS ONE. 7 (11) e50253. https://doi.org/10.1371/journal.pone.0050253

Identification of Schistosoma mansoni microRNAs
Simões, M.C., Lee, J., Djikeng, A., Cerqueira, G.C., Zerlotini, A., da Silva-Pereira, R.A., Dalby, A.R., LoVerde, P., El-Sayed, N.M. and Oliveira, G. 2011. Identification of Schistosoma mansoni microRNAs. BMC Genomics. 12 (47), pp. 1-17. https://doi.org/10.1186/1471-2164-12-47

Developing stochastic models for spatial inference: bacterial chemotaxis
Yu, Y.D., Choi, Y., Teo, Y.Y. and Dalby, A.R. 2010. Developing stochastic models for spatial inference: bacterial chemotaxis. PLoS ONE. 5 (5) e10464. https://doi.org/10.1371/journal.pone.0010464

A comparative proteomic analysis of the simple aminoacid repeat distributions in Plasmodia reveals lineagespecific amino acid selection
Dalby, A.R. 2009. A comparative proteomic analysis of the simple aminoacid repeat distributions in Plasmodia reveals lineagespecific amino acid selection. PLoS ONE. 4 (7) e6231. https://doi.org/10.1371/journal.pone.0006231

Beta-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of beta-sheet elongation by proline residues in human prion protein.
Shamsir, M.S. and Dalby, A.R. 2007. Beta-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of beta-sheet elongation by proline residues in human prion protein. Biophysical Journal. 92 (6), pp. P2080-2089. https://doi.org/10.1529/biophysj.106.092320

COPASAAR--a database for proteomic analysis of single amino acid repeats.
Depledge, D.P. and Dalby, A.R. 2005. COPASAAR--a database for proteomic analysis of single amino acid repeats. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-6-196

Predicting the phosphorylation sites using hidden Markov models and machine learning methods.
Senawongse, P., Dalby, A.R. and Yang, Z.R. 2005. Predicting the phosphorylation sites using hidden Markov models and machine learning methods. Journal of Chemical Information and Modeling. 45 (4), pp. 1147-1152. https://doi.org/10.1021/ci050047+

Evaluation of mutual information and genetic programming for feature selection in QSAR.
Venkatraman, V., Dalby, A.R. and Yang, Z.R. 2004. Evaluation of mutual information and genetic programming for feature selection in QSAR. Journal of Chemical Information and Computer Sciences. 44 (5), pp. 1686-1692. https://doi.org/10.1021/ci049933v

Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms.
Berry, E.A., Dalby, A.R. and Yang, Z.R. 2004. Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms. Computational Biology and Chemistry. 28 (1), pp. 75-85. https://doi.org/10.1016/j.compbiolchem.2003.11.005

Constructing an enzyme-centric view of metabolism.
Horne, A.B., Hodgman, T.C., Spence, H.D. and Dalby, A.R. 2004. Constructing an enzyme-centric view of metabolism. Bioinformatics. 20 (13), pp. 2050-2055. https://doi.org/10.1093/bioinformatics/bth199

Mining HIV protease cleavage data using genetic programming with a sum-product function.
Yang, Z.R., Dalby, A.R. and Qiu, J. 2004. Mining HIV protease cleavage data using genetic programming with a sum-product function. Bioinformatics. 20 (18), pp. 3398-3405. https://doi.org/10.1093/bioinformatics/bth414

The structure of human liver fructose-1,6-bisphosphate aldolase
Dalby, A.R., Tolan, D.R. and Littlechild, J.A. 2002. The structure of human liver fructose-1,6-bisphosphate aldolase. Acta Crystallographica Section D. D57, pp. 1526-1533. https://doi.org/10.1107/s0907444901012719

Structural and functional comparisons between vanadium haloperoxidase and acid phosphatase enzymes.
Littlechild, J., Garcia-Rodriguez, E., Dalby, A.R. and Isupov, M. 2002. Structural and functional comparisons between vanadium haloperoxidase and acid phosphatase enzymes. Journal of Molecular Recognition. 15 (5), pp. 291-296. https://doi.org/10.1002/jmr.590

Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis.
Isupov, M.N., Dalby, A.R., Brindley, A.A., Izumi, Y., Tanabe, T., Murshudov, G.N. and Littlechild, J.A. 2000. Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis. Journal of Molecular Biology. 299 (4), pp. 1035-1049. https://doi.org/10.1006/jmbi.2000.3806

Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications.
Dalby, A.R., Dauter, Z. and Littlechild, J.A. 1999. Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications. Protein Science. 8 (2), pp. 291-297. https://doi.org/10.1110/ps.8.2.291

Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.
Crowhurst, G.S., Dalby, A.R., Isupov, M.N., Campbell, J.W. and Littlechild, J.A. 1999. Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A. Acta Crystallographica Section D. D55, pp. 1822-1826. https://doi.org/10.1107/s0907444999009944

Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis.
Brindley, A.A., Dalby, A.R., Isupov, M.N. and Littlechild, J.A. 1998. Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis. Acta Crystallographica Section D: Structural Biology. D54 (Pt 3), pp. 454-457. https://doi.org/10.1107/s0907444997014558

Studies with type I aldolase to understand fructose intolerance and combat parasitic disease.
Dalby, A.R. and Littlechild, J.A. 1996. Studies with type I aldolase to understand fructose intolerance and combat parasitic disease. Journal of Pharmacy and Pharmacology. 48 (2), pp. 214-217. https://doi.org/10.1111/j.2042-7158.1996.tb07126.x

Permalink - https://westminsterresearch.westminster.ac.uk/item/95621/a-global-phylogenetic-analysis-in-order-to-determine-the-host-species-and-geography-dependent-features-present-in-the-evolution-of-avian-h9n2-influenza-hemagglutinin


Share this

Usage statistics

62 total views
135 total downloads
These values cover views and downloads from WestminsterResearch and are for the period from September 2nd 2018, when this repository was created.