NS  Vol.4 No.11 , November 2012
Phylogenetic analysis of the five internal genes and evolutionary pathways of the Greek H3N8 equine influenza virus
Abstract: To amplify the NS, NP, PB1, PB2 and PA internal genes of two equine H3N8 influenza A viruses isolated in Greece in 2003 and 2007 five primer pairs were designed. The derived sequences were analysed from a phylogenetic point of view and compared with the evolutionary patters of the HA and NA proteins. Comparison of nucleotide sequences of the five internal genes of the Greek strains showed high similarity (99.3% - 99.7%) to strains isolated from outbreaks in Europe and Asia during 2002-2008. A total of 11 amino acid substitutions of the surface protein NA and the RNP complex proteins were identified in the Greek strains compared to those of progenitor viruses circulating up to 2003. These substitutions were repeated in Chinese and Mongolian isolates from outbreaks in 2007-2008. Notably NS1 protein did not acquired amino acid substitutions and moreover, a stop codon introduced at position 220 was stably maintained in the Greek strains. Phylogenetic trees of the five internal genes did not show the same separation in clades. Greek strains classified them into the American sublineage (as for the PA) Florida clade II (as for the NP, NS1 and PB1) and among Chinese strains of 2007-2008 outbreaks (as for the PB2). Additionally, evolutionary profiles of these internal proteins, except PB2, indicated a parallel evolution fashion to the HA protein, suggesting the possible occurrence of genetic reassortment between H3N8 viruses of district evolutionary lineages. In conclusion, phylogenetic analysis of the internal genes reported in this study could establish a candidate framework for future scientific communications on the phylogenetic diversity and evolution of the equine influenza viruses.
Cite this paper: Bountouri, M. , Ntafis, V. , Fragkiadaki, E. , Kanellos, T. and Xylouri, E. (2012) Phylogenetic analysis of the five internal genes and evolutionary pathways of the Greek H3N8 equine influenza virus. Natural Science, 4, 839-847. doi: 10.4236/ns.2012.411112.

[1]   Ito, M., Nagai, M., Hayakawa, Y., Komae, H., Murakami, N., Yotsuya, S., Asakura, S., Sakoda, Y. and Kida, H. (2008) Genetic analyses of an H3N8 influenza virus isolate, causative strain of the outbreak of equine influenza at the Kanazawa racecourse in Japan in 2007. Journal of Veterinary Medical Science, 70, 899-906. doi:10.1292/jvms.70.899

[2]   Anon, (2008) Summary of the Australian equine influenza outbreak. Veterinary Record, 163, 378. doi:10.1136/vr.163.13.378

[3]   Webster, R.G., Bean, W.J., Gorman, O.T., Chambers, T.M. and Kawaoka, Y. (1992) Evolution and ecology of influenza A viruses. Microbiological Review, 56, 152-179.

[4]   Bryant, N.A., Rash, A.S., Russell, C.A., Ross, J., Cooke, A., Bowman, S., Shona MacRae, A., Lewis, N.S., Paillot, R., Zanoni, R., Meier, H., Griffiths, L.A., Daly, J.M., Tiwari, A., Chambers, T.M., Newton, J.R. and Elton, D.M. (2009) Antigenic and genetic variations in European and North American equine influenza virus strains (H3N8) isolated from 2006 to 2007. Veterinary Microbiology, 38, 41-52. doi:10.1016/j.vetmic.2009.03.004

[5]   Bountouri, M., Fragkiadaki, E., Ntafis, V., Kanellos, T. and Xylouri, E. (2011) Phylogenetic and molecular characterization of equine H3N8 influenza viruses from Greece (2003 and 2007): Evidence for reassortment between evolutionary lineages. Virology Journal, 8, 350. doi:10.1186/1743-422X-8-350

[6]   Endo, A., Pecoraro, R., Sugita, S. and Nerome, K. (1992) Evolutionary pattern of the H3 haemagglutinin of equine influenza viruses: multiple evolutionary lineages and frozen replication. Archives of Virology, 123, 73-87. doi:10.1007/BF01317139

[7]   Wright, P. F. and Webster, R.G. (2001) Orthomyxoviruses. In: Fields, B.N. and Knipe, D.M. Eds., Fields Virology, 4th Edition, Lippincott Williams & Wilkins, Philadelphia, 1533-1579.

[8]   Hall, T.A. (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95- 98.

[9]   Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 4, 1596-1599. doi:10.1093/molbev/msm092

[10]   Qi, T., Guo, W., Huang, W.-Q., Li, H.-M., Zhao, L.-P., Dai, L.-L., He, N., Hao, X.-F. and Xiang, W.-H. (2010) Genetic evolution of equine influenza viruses isolated in China. Archives of Virology, 155, 1425-1432. doi:10.1007/s00705-010-0724-y

[11]   Neumann, G. and Kawaoka, Y. (2006) Host range restricttion and pathogenicity in the context of influenza pandemic. Emerging Infectious Diseases, 12, 881-886. doi:10.3201/eid1206.051336

[12]   Jackson, D., Hossain, M.J., Hickman, D., Perez, D.R. and Lamb, R.A. (2008) A new influenza virus virulence determinant: The NS1 protein four C-terminal residues modulate pathogenicity. Proceedings of the National Academy of Sciences of the United States of America, 105, 4381- 4386. doi:10.1073/pnas.0800482105

[13]   Jemth, P. and Gianni, S. (2007) PDZ domains: Folding and binding. Biochemistry, 46, 8701-8708. doi:10.1021/bi7008618

[14]   Gorman, O.T., Bean, W., Kawaoka, Y. and Webster, R. (1990) Evolution of the nucleoprotein gene of influenza A virus. Journal of Virology, 64, 1487-1497.

[15]   Gorman, O.T., Donis, R., Kawaoka, Y. and Webster, R. (1990) Evolution of influenza A virus PB2 genes: Implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus. Journal of Virology, 64, 4893-4902.

[16]   Rivailler, P., Perry, I.A., Jang, Y., Davis, C.T., Chen, L.M., Dubovi, E.J. and Donis, R.O. (2010) Evolution of canine and equine influenza (H3N8) viruses co-circulating between 2005 and 2008. Virology, 408, 71-79. doi:10.1016/j.virol.2010.08.022

[17]   Guilligay, D., Tarendeau, F., Resa-Infante, P., Coloma, R., Crepin, T., Sehr, P., Lewis, J., Ruigrok, R.W., Ortin, J., Hart, D.J. and Cusack, S. (2008) The structural basis for cap binding by influenza virus polymerase subunit PB2. Nature Structural & Molecular Biology, 15, 500-506. doi:10.1038/nsmb.1421