Modeling the Avian Influenza H5N1 Virus Infection in Human and Analyzing Its Evolution

  • Ping ZhangEmail author
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 699)


Here, after identifying the HPAI H5N1 gene data corresponding to the sites of HPAI H5N1 outbreaks in poultry and wild birds, the outbreak locations were set as the sources of human infection and a patch-based SEIR Cellular Automata (CA) epidemic model was run to simulate human responses to the HPAI H5N1 virus. HPAI H5N1 viruses from poultry and wild birds that were capable of infecting humans were identified and, through reconstruction of the phylogenetic trees with estimation of the evolutionary distances, the evolution of the HPAI H5N1 virus capable of infecting humans transmitted through poultry and wild birds was analyzed. HPAI H5N1 transmission between poultry and humans in China was modeled in different human population density scenarios from 2004–2009. The results showed that different human density distributions had little effect on the number of human cases of HPAI H5N1 and that poultry was the main source of infection.


Patch-based SEIR CA epidemic model Phylogenetic tree Human density distribution H5N1 


  1. 1.
    Ku, A., Chan, L.: The first case of H5N1 avian influenza infection in a human with complications of adult respiratory distress syndrome and Reye’s syndrome. J. Paediatr. Child Health 35, 207–209 (1999)CrossRefGoogle Scholar
  2. 2.
    World Health Organization.
  3. 3.
    Watanabe, Y., Ibrahim, M.S., Suzuki, Y., Ikuta, K.: The changing nature of avian influenza A virus (H5N1). Trends Microbiol. 20(1), 11–20 (2012)CrossRefGoogle Scholar
  4. 4.
    Shu, Y., Yu, H., Li, D.: Lethal avian influenza A (H5N1) infection in a pregnant woman in Anhui Province, China. N. Engl. J. Med. 354, 1421–1422 (2006)CrossRefGoogle Scholar
  5. 5.
    Wang, H., Feng, Z., Shu, Y., Yu, H., Zhou, L., Zu, R., Huai, Y., Dong, J., Bao, C., Wen, L., Wang, H., Yang, P., Zhao, W., Dong, L., Zhou, M., Liao, Q., Yang, H., Wang, M., Lu, X., Shi, Z., Wang, W., Gu, L., Zhu, F., Li, Q., Yin, W., Yang, W., Li, D., Uyeki, T.M., Wang, Y.: Probable limited person-to-person transmission of highly pathogenic avian influenza A (H5N1) virus in China. Lancet 371, 1427–1434 (2008)CrossRefGoogle Scholar
  6. 6.
    Neumann, G., Chen, H., Gao, G.F., Shu, Y., Kawaoka, Y.: H5N1 influenza viruses: outbreaks and biological properties. Cell Res. 20, 51–61 (2010)CrossRefGoogle Scholar
  7. 7.
    Yang, Y., Halloran, M.E., Sugimoto, J.D., Longini Jr., I.M.: Detecting human-to-human transmission of avian influenza A (H5N1). Emerg. Infect. Dis. 13(9), 1348–1353 (2007)CrossRefGoogle Scholar
  8. 8.
    Iwami, S., Takeuchi, Y., Liu, X.: Avian flu pandemic: can we prevent it? J. Theor. Biol. 257, 181–190 (2009)MathSciNetCrossRefGoogle Scholar
  9. 9.
    Horimoto, T., Kawaoka, Y.: Influenza: lessons from past pandemics, warnings from current incidents. Nat. Rev. Microbiol. 3, 591–600 (2005)CrossRefGoogle Scholar
  10. 10.
    Liu, J., Xiao, H., Lei, F., Zhu, Q., Qin, K., Zhang, X.W., Zhang, X.L., Zhao, D., Wang, G., Feng, Y., Ma, J., Liu, W., Wang, J., Gao, G.F.: Highly pathogenic H5N1 influenza virus infection in migratory birds. Science 309, 1206 (2005)CrossRefGoogle Scholar
  11. 11.
    Keawcharoen, J., Oraveerakul, K., Kuiken, T., Fouchier, R.A.M., Amonsin, A., Payungporn, S., Noppornpanth, S.: Avian influenza H5N1 in tigers and leopards. Emerg. Infect. Dis. 10, 2189–2191 (2004)CrossRefGoogle Scholar
  12. 12.
    de Jong, M.D., Hien, T.T.: Avian influenza A (H5N1). J. Clin. Virol. 35, 2–13 (2006)CrossRefGoogle Scholar
  13. 13.
    Roberton, S.I., Bell, D.J., Smith, G.J.D., Nicholls, J.M., Chan, K.H., Nguyen, D.T., Tran, P.Q., Streicher, U., Poon, L.L.M., Chen, H., Horby, P., Guardo, M., Guan, Y., Peiris, J.S.M.: Avian influenza H5N1 in viverrids: implications for wildlife health and conservation. Proc. Biol. Sci. 273, 1729–1732 (2006)CrossRefGoogle Scholar
  14. 14.
    Abdel-Moneim, A.S., Abdel-Ghany, A.E., Shany, S.A.S.: Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkey. J. Biomed. Sci. 17, 25 (2000)CrossRefGoogle Scholar
  15. 15.
    Watanabe, Y., Ibrahim, M.S., Ellakany, H.F., Kawashita, N., Mizuike, R., Hiramatsu, H., Sriwilaijaroen, N., Takagi, T., Suzuki, Y., Ikuta, K.: Acquisition of human-type receptor binding specificity by new H5N1 influenza virus sublineages during their emergence in birds in Egypt. PLoS Pathog. 7, e1002068 (2011)CrossRefGoogle Scholar
  16. 16.
    Webster, R.G., Bean, W.J., Gorman, O.T., Chambers, T.M., Kawaoka, Y.: Evolution and ecology of influenza A viruses. Microbiol. Rev. 56, 152–179 (1992)Google Scholar
  17. 17.
    Taubenberger, J.K., Reid, A.H., Lourens, R.M., Wang, R., Jin, G., Fanning, T.G.: Characterization of the 1918 influenza virus polymerase genes. Nature 437, 889–893 (2005)CrossRefGoogle Scholar
  18. 18.
    Smith, D.J.: Predictability and preparedness in influenza control. Science 312, 392–394 (2006)CrossRefGoogle Scholar
  19. 19.
    Iwami, S., Takeuchi, Y., Liu, X.: Avian-human influenza epidemic model. Math. Biosci. 207, 1–25 (2007)MathSciNetCrossRefzbMATHGoogle Scholar
  20. 20.
    Kim, K.I., Lin, Z., Zhang, L.: Avian-human influenza epidemic model with diffusion. Nonlinear Anal.: Real World Appl. 11, 313–322 (2010)MathSciNetCrossRefzbMATHGoogle Scholar
  21. 21.
    Agarwal, M., Verma, V.: An avian-human influenza epidemic model with vaccination. J. Appl. Sci. 5(6), 451–458 (2010)Google Scholar
  22. 22.
    Samanta, G.P.: Permanence and extinction for anonautonomous avian-human influenza epidemic model with distributed time delay. Math. Comput. Model. 52, 1794–1811 (2010)CrossRefzbMATHGoogle Scholar
  23. 23.
    Lucchetti, J., Roy, M., Martcheva, M.: An avian influenza model and its fit to human avian influenza cases. In: Tchuenche, J.M., Mukandavire, Z. (eds.) Advances in Disease Epidemiology, pp. 1–30. Nova Science Publishers, New York (2009)Google Scholar
  24. 24.
    Drummond, A.J., Ho, S.Y.W., Phillips, M.J., Rambaut, A.: Relaxed phylogenetics and dating with confidence. PLoS Biol. 4(5), e88 (2006)CrossRefGoogle Scholar
  25. 25.
    Vibound, C., Bjørnstad, O.N., Smith, D.L., Simonsen, L., Miller, M.A., Grenfell, B.T.: Synchrony, waves, and spatial hierarchies in the spread of influenza. Science 312, 447–451 (2006)CrossRefGoogle Scholar
  26. 26.
    Ghedin, E., Sengamalay, N.A., Shumway, M., Zaborsky, J., Feldblyum, T., Subbu, V., Spiro, D.J., Sitz, J., Koo, H., Bolotov, P., Dernovoy, D., Tatusova, T., Bao, Y., George, K.S., Taylor, J., Lipman, D.J., Fraser, C.M., Taubenberger, J.K., Salzberg, S.L.: Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437, 1162–1166 (2005)CrossRefGoogle Scholar
  27. 27.
    Nelson, M.I., Holmes, E.C.: The evolution of epidemic influenza. Nat. Rev. 8, 196–205 (2007)CrossRefGoogle Scholar
  28. 28.
    Ferguson, N.M., Galvani, A.P., Bush, R.M.: Ecological and immunological determinants of influenza evolution. Nature 422, 428–433 (2003)CrossRefGoogle Scholar
  29. 29.
    Koelle, K., Cobey, S., Grenfell, B., Pascual, M.: Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314, 1898–1903 (2006)CrossRefGoogle Scholar
  30. 30.
    Koelle, K., Khatri, P., Kamradt, M., Kepler, T.B.: A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. J. R. Soc. Interface 7, 1257–1274 (2010)CrossRefGoogle Scholar
  31. 31.
    Roche, B., Drake, J.M., Rohani, P.: An agent-based model to study the epidemiological and evolutionary dynamics of influenza viruses. BMC Bioinform. 12, 87 (2011)CrossRefGoogle Scholar
  32. 32.
    Martcheva, M.: An evolutionary model of influenza A with drift and shift. J. Biol. Dyn. 6(2), 299–332 (2011)MathSciNetCrossRefGoogle Scholar
  33. 33.
    Ito, K., Igarashi, M., Miyazaki, Y., Murakami, T., Iida, S., Kida, H., Takada, A.: Gnarled-trunk evolutionary model of influenza A virus hemagglutinin. PLoS ONE 6(10), e25953 (2011)CrossRefGoogle Scholar
  34. 34.
    World Organization for Animal Health.
  35. 35.
  36. 36.
    Data Sharing Infrastructure of Earth System Science.
  37. 37.
    Landscan Global Population Project.
  38. 38.
    China Statistics Yearbook.
  39. 39.
    National Center for Biotechnology Information.
  40. 40.
  41. 41.
    van den Driessche, P.: Spatial structure: patch models. In: Brauer, F., van den Driessche, P., Wu, J. (eds.) Mathematical Epidemiology, pp. 179–189. Springer, Berlin (2008). (Chapt. 7)CrossRefGoogle Scholar
  42. 42.
    Sirakoulis, GCh., Karafyllidis, I., Thanailakis, A.: A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecol. Model. 133, 209–223 (2000)CrossRefGoogle Scholar
  43. 43.
    Zhang, P., Atkinson, P.M.: Modelling the effect of urbanization on the transmission of an infectious disease. Math. Biosci. 211, 166–185 (2008)MathSciNetCrossRefzbMATHGoogle Scholar
  44. 44.
    Nei, M., Kumar, S.: Phylogenetic trees. In: Nei, M., Kumar, S. (eds.) Molecular evolution and phylogenetics, pp. 73–86. Oxford University Press, New York (2000). (Chap. 5)Google Scholar
  45. 45.
    Li, S., Pearl, D.K., Doss, H.: Phylogenetic tree construction using Markov Chain Monte Carlo. J. Am. Stat. Assoc. 95(450), 493–508 (2000)CrossRefGoogle Scholar
  46. 46.
    Yang, Z.: Phylogenetic analysis using parsimony and likelihood methods. J. Mol. Evol. 42, 294–307 (1996)CrossRefGoogle Scholar
  47. 47.
    Saitou, N.: Property and efficiency of the maximum likelihood method for molecular phylogeny. J. Mol. Evol. 27, 261–273 (1988)CrossRefGoogle Scholar
  48. 48.
    Attwood, T.K., Parry-Smith, D.J.: Multiple sequence alignment. In: Introduction to Bioinformatics. Addison Wesley Longman Limited, London (1999). (Chap. 7)Google Scholar
  49. 49.
    Nei, M., Kumar, S.: Evolutionary change of amino acid sequences. In: Nei, M., Kumar, S. (eds.) Molecular evolution and phylogenetics, pp. 17–32. Oxford University Press, New York (2000). (Chapt. 2)Google Scholar
  50. 50.
  51. 51.
    O’Sullivan, D., Torrens, P.M.: Cellular models of urban systems. CASA Paper 22 (2000)Google Scholar
  52. 52.
    Small, M., Walker, D.M., Tse, C.K.: Scale-free distribution of avian influenza outbreaks. Phys. Rev. Lett. 99, 188702 (2007)CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  1. 1.Geo-Exploration Science and Technology CollegeJilin UniversityChangchunChina

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