Receptor binding specificity and origin of 2009 H1N1 pandemic influenza virus

Wei Hu

.

DOI: 10.4236/ns.2011.33030                

Abstract

Recently, a genetic variant of 2009 H1N1 has become the predominant virus circulating in the southern hemisphere, particularly Australia and New Zealand, and in Singapore during the winter of 2010. It was associated with several vaccine breakthroughs and fatal cases. We analyzed three reported mutations D94N, N125D, and V250A in the HA protein of this genetic variant. It appeared that the reason for D94N and V250A to occur in pairs was to maintain the HA binding to human type receptor, so the virus could replicate in humans efficiently. Guided by this interpretation, we discovered a new mutation V30A that could compensate for N125D as V250A did for D94N. We demonstrated that the presence of amino acids 30A and 125N in HA enhanced the binding to human type receptor, while 30V and 125D favored the receptors of avian type and of A/South Carolina/1/18 (H1N1). Furthermore, a combination of 94D, 125D, and 250V made the primary binding preference similar to that of A/South Carolina/1/18 (H1N1) and a combination of 94N, 125D, and 250A resulted in the primary binding affinity for avian type receptor, which clearly differed from that of A/California/07/2009 (H1N1), a strain used in the vaccine for 2009 H1N1. We also re-examined the origin of 2009 H1N1 to refine our knowledge of this important issue. Although the NP, PA, PB1, and PB2 of 2009 H1N1 were closest to North American swine H3N2 in sequence identity, their interaction patterns were closest to swine H1N1 in North America.

Keywords

2009 H1N1; Hemagglutinin; Influenza; Informational Spectrum Method; Mutation; Receptor Binding Specificity

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Garten, R.J., Davis, C.T., Russell, C.A., Shu, B., Lindstrom, S., Balish, A., et al. (2009) Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science, 325, 197-201. doi:10.1126/science.1176225
[2]	Hu, W. (2009) Analysis of correlated mutations, stalk motifs, and phylogenetic relationship of the 2009 influenza A virus neuraminidase sequences. Journal of Biomedical Science and Engineering, 2, 550-558. doi:10.4236/jbise.2009.27080
[3]	Hu, W. (2010) The Interaction between the 2009 H1N1 influenza A hemagglutinin and neuraminidase: Mutations, co-mutations, and the NA stalk motifs. Journal of Biomedical Science and Engineering, 3, 1-12.
[4]	Hu, W. (2010) Novel host markers in the 2009 pandemic H1N1 influenza A virus. Journal of Biomedical Science and Engineering, 3, 584-601. doi:10.4236/jbise.2010.36081
[5]	Hu, W. (2010) Nucleotide host markers in the influenza A viruses. Journal of Biomedical Science and Engineering, 3, 684-699. doi:10.4236/jbise.2010.37093
[6]	Hu, W. (2010) Identification of highly conserved domains in hemagglutinin associated with the receptor binding specificity of influenza viruses: 2009 H1N1, Avian H5N1, and Swine H1N2. Journal of Biomedical Science and Engineering, 3, 114-123. doi:10.4236/jbise.2010.32017
[7]	Hu, W. (2010) Quantifying the effects of mutations on receptor binding specificity of influenza viruses. Journal of Biomedical Science and Engineering, 3, 227-240. doi:10.4236/jbise.2010.33031
[8]	Hu, W. (2010) Subtle differences in receptor binding specificity and gene sequences of the 2009 pandemic H1N1 influenza virus. Advances in Bioscience and Biotechnology, 1, 305-314. doi:10.4236/abb.2010.14040
[9]	Hu, W. (2010) Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2. Natural Science, 2, 1138-1147. doi:10.4236/ns.2010.210141
[10]	King, D., Miller, Z., Jones, W. and Hu, W. (2010) Characteristic sites in the internal proteins of avian and human influenza viruses. Journal of Biomedical Science and Engineering, 3, 943-955. doi:10.4236/jbise.2010.310125
[11]	Hu, W. (2010) Highly conserved domains in hemagglutinin of influenza viruses characterizing dual receptor binding. Natural Science, 2, 1005-1014. doi:10.4236/ns.2009.29123
[12]	Hu, W. (2010) Host markers and correlated mutations in the overlapping genes of influenza viruses: M1, M2; NS1, NS2; and PB1, PB1-F2. Natural Science, 2, 1225-1246. doi:10.4236/ns.2010.211150
[13]	Barr, I.G., Cui, L., Komadina, N., Lee, R.T., Lin, R.T., Deng, Y., Caldwell, N., Shaw, R. and Maurer-Stroh, S. (2010) A new pandemic influenza A(H1N1) genetic variant predominated in the winter 2010 influenza season in Australia, New Zealand and Singapore. Euro Surveill, 15, 19692.
[14]	Stevens, J., Blixt, O., Glaser, L., Taubenberger, J.K., Palese, P., Paulson, J.C. and Wilson, I.A. (2006) Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. Journal of Molecular Biology, 355: 1143- 1155. doi:10.1016/j.jmb.2005.11.002
[15]	Stevens, J., Blixt, O., Tumpey, T.M., Taubenberger, J.K., Paulson, J.C. and Wilson, I.A. (2006) Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science, 312, 404-410. doi:10.1126/science.1124513
[16]	Matrosovich, M., Tuzikov, A., Bovin, N., Gambaryan, A., Klimov, A., Castrucci, M.R., Donatelli, I. and Kawaoka, Y. (2000) Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals. Journal of Virology, 74, 8502-8512. doi:10.1128/JVI.74.18.8502-8512.2000
[17]	Karasin, A.I., West, K., Carman, S. and Olsen, C.W. (2004) Characterization of avian H3N3 and H1N1 influenza A viruses isolated from pigs in Canada. Journal of Clinical Microbiology, 42, 4349-4354. doi:10.1128/JCM.42.9.4349-4354.2004
[18]	Liu, Y., Childs, R.A., Matrosovich, T., Wharton, S., Palma, A.S., Chai, W., Daniels, R., Gregory, V., et al. (2010). Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus. Journal of Virology, 84, 12069-12074. doi:10.1128/JVI.01639-10
[19]	Kilander, A., Rykkvin, R., Dudman, S. and Hungnes, O. (2010) Observed association between the HA1 mutation D222G in the 2009 pandemic influenza A(H1N1) virus and severe clinical outcome, Norway 2009-2010. Euro Surveill, 15, 19498.
[20]	Liu, Y., Childs, R.A., Matrosovich, T., et al. (2010) Altered receptor specificity and cell tropism of D222G Hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus. Journal of Virology, 84, 12069-12074. doi:10.1128/JVI.01639-10
[21]	Su, Y. Yang, H.Y., Zhang, B.J., Jia, H.L. and Tien, P. (2008) Analysis of a point mutation in H5N1 avian influenza virus haemagglutinin in relation to virus entry into live mammalian cells. Archives of Virology, 153, 2253-2261. doi:10.1007/s00705-008-0255-y
[22]	Veljkovic, V., Niman, H.L., Glisic, S., Veljkovic, N., Perovic, V. and Muller, C.P. (2009) Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor. BMC Structural Biology, 9, 62. doi:10.1186/1472-6807-9-62
[23]	Veljkovic, V., Veljkovic, N., Muller, C.P., Müller, S., Glisic, S., Perovic, V. and K?hler, H. (2009) Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control. BMC Structural Biology, 7, 9-21.
[24]	Veljkovic, N., Glisic, S., Prljic, J., Perovic, V., Botta, M. andVeljkovic, V. (2008) Discovery of new therapeutic targets by the informational spectrum method. Current Protein and Peptide Science, 9, 493-506. doi:10.2174/138920308785915245
[25]	Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33, 511- 518. doi:10.1093/nar/gki198
[26]	Cosic, I. (1997) The resonant recognition model of macromolecular bioreactivity, theory and application. Birkhauser Verlag, Berlin.
[27]	http://www.cdc.gov/flu/about/qa/1011_vac_selection.htm
[28]	Solovyov, A., Palacios, G., Briese, T., Lipkin, W.I. and Rabadan, R. (2009) Cluster analysis of the origins of the new influenza A(H1N1) virus. European Surveillance, 14, 19224.
[29]	Wong, E.H., Smith, D.K., Rabadan, R., Peiris, M. and Poon, L.L. (2010) Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evolutionary Biology, 10, 253. doi:10.1186/1471-2148-10-253
[30]	Wanitchang, A., Jengarn, J. and Jongkaewwattana, A. (2011) The N terminus of PA polymerase of swine-origin influenza virus H1N1 determines its compatibility with PB2 and PB1 subunits through a strain-specific amino acid serine 186. Virus Research, 155, 325-333. doi:10.1016/j.virusres.2010.10.032
[31]	Mehle, A. and Doudna, J.A. (2009) Adaptive strategies of the influenza virus polymerase for replication in humans. Proceedings of National Academy Science of U.S.A., 106: 21312-21316. doi:10.1073/pnas.0911915106
[32]	Maurer-Stroh, S., Lee, R.T., Eisenhaber, F., Cui, L., Phuah, S.P. and Lin, R.T. (2010) A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. PLoS Currency, RRN1162.