Novel Phylogenetic Algorithm to Monitor Human Tropism in Egyptian H5N1-HPAIV Reveals Evolution toward Efficient Human-to-Human Transmission

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Perovic, Vladimir R ^a   Muller, Claude P ^b   Niman, Henry L ^c   Veljkovic, Nevena ^a   Dietrich, Ursula ^d   Tosic, Dusan D ^e   Glisic, Sanja ^a   Veljkovic, Veljko ^a  

^a UNIVERSITY OF BELGRADE   (Serbia)

^b LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^c Recombinomics Inc   (United States)

^d INSTITUTE FOR TUMOR BIOLOGY AND EXPERIMENTAL THERAPY   (Germany)

^e UNIVERSITY OF BELGRADE   (Serbia)

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VIRUS HEMAGGLUTININ;

ARTICLE; CONTROLLED STUDY; EGYPT; GENETIC ALGORITHM; HUMAN; INFLUENZA A (H5N1); INFLUENZA VIRUS A H5N1; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PREDICTION; PREVALENCE; TROPISM; VIRUS ISOLATION; VIRUS MUTATION; VIRUS STRAIN; VIRUS TRANSMISSION;

ALGORITHMS; ANIMALS; CHICKENS; EGYPT; EPIDEMIOLOGICAL MONITORING; EVOLUTION, MOLECULAR; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MUTATION; PANDEMICS; PHYLOGENY; RECEPTORS, VIRUS; VIRAL TROPISM; VIRULENCE;

AVES;

EID: 84876823956     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0061572     Document Type: Article

References (46)

1. Bahgat MM, Kutkat MA, Nasraa MH, Mostafa A, Webby R, et al. (2009) Characterization of an avian influenza virus H5N1 Egyptian isolate. J Virol Methods 59: 244-250.
2. Aly MM, Arafa A, Hassan MK, (2008) Epidemiological findings of outbreaks of disease caused by highly pathogenic H5N1 avian influenza virus in poultry in Egypt during 2006. Avian Dis 52: 269-277.
3. World Health Organization (WHO) website. Influenza at the Human-Animal Interface (HAI). Available: http://www.who.int/influenza/human_animal_interface/en/. Accessed 2012 Nov 3.
4. Epstein S, (2012) T-cell immune responses and asymptomatic H5N1 influenza infection. J Infect Dis 205: 4-6.
5. Veljkovic V, Veljkovic N, Muller CP, Müller S, Glisic S, et al. (2009) Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control. BMC Struct Biol 9: 21.
6. Veljkovic V, Niman HL, Glisic S, Veljkovic N, Perovic V, et al. (2009) Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor. BMC Struct Biol 9: 62.
7. Veljkovic N, Glisic S, Prljic J, Perovic V, Botta M, et al. (2008) Discovery of new therapeutic targets by the informational spectrum method. Curr Protein Pept Sci 9: 493-506.
8. Veljkovic V, Veljkovic N, Este JA, Huther A, Dietrich U, (2007) Application of the EIIP/ISM bioinformatics concept in development of new drugs. Curr Med Chem 14: 441-453.
9. National Center for Biotechnology Information (NCBI) database. Available: http://ncbi.nlm.nih.gov/protein. Accessed 2012 Nov 15.
10. Global Initiative on Sharing All Influenza Data (GISAID) database Available: http://platform.gisaid.org.Accessed 2012 Nov 15.
11. Veljkovic V (1980) Theoretical approach to preselection of cancerogens and chemical carcinogenesis. Gordon & Breach, New York.
12. Veljkovic V, Slavic I, (1972) Simple general-model pseudopotential. Phys Rev Lett 29: 105-106.
13. Veljkovic V, (1973) The dependence of the Fermi energy on the atomic number. Phys Lett 45A: 41-42.
14. Veljkovic V, Cosic I, Dimitrijevic B, Lalovic D, (1983) Is it possible to analyze DNA and protein sequence by the method of digital signal processing? IEEE Trans BME-32: 337-340.
15. David WM (2001) Bioinformatics: sequence and genome analysis. Cold Spring Harbor Laboratory Press. 6.
16. Fitch WM, (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 35: 406-416.
17. Sankoff D, Cedergren RJ, (1983) Simultaneous comparison of three or more sequences related by a tree. In Sankoff D, Kruskal JR,et al. (1983) Time warps, string edits, and macromolecules: The theory and practice of sequence comparison. Addison-Wesley 9: 253-264.
18. Feng DF, Doolittle RF, (1996) Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. Methods Enzymol 266: 368-382.
19. Jukes TH, Cantor CR (1969) Mammalian Protein Metabolism, Academic Press: 21-132.
20. Kimura M, (1980) A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
21. Fitch WM, Margoliash E, (1987) Construction of phylogenetic trees. Science 155: 279-284.
22. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
23. Felsenstein J, (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22: 240-249.
24. Mau B, Newton MA, Larget B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Technical Report 961, Statistics Department, university of Wisconsin-Madison.
25. Open Web Server for Informational Spectrum-based Phylogenetic Analysis (ISTREE). Available: http://istree.bioprotection.org/. Accessed 2012 Nov 15.
26. Watanabe Y, Ibrahim MS, Ellakany HF, Kawashita N, Mizuike R, et al. (2011) Acquisition of human-type receptor binding specificity by new H5N1 influenza virus sublineages during their emergence in birds in Egypt. PLoS Pathog 7: e1002068.
27. Kayali G, Webby RJ, Ducatez MF, El Shesheny RA, Kandeil AM, et al. (2011) The epidemiological and molecular aspects of influenza H5N1 virus at the human-animal interface in Egypt. PLoS One 6: e17730.
28. Li Z, Zhonghua Liu Z, Ma C, Zhang L, Su Y, et al. (2011) Identification of amino acids in highly pathogenic avian influenza H5N1 virus hemagglutinin that determine avian influenza species specificity. Arch Virol 156: 1803-1812.
29. Kongchanagul A, Suptawiwat O, Pumaree Kanrai P, Uiprasertkul M, Pilaipan Puthavathana P, et al. (2008) Positive selection at the receptor-binding site of haemagglutinin H5 in viral sequences derived from human tissues. J Gen Virol 89: 1805-1810.
30. Abdelwhab EM, Hafez HM, Aly MM, Grund C, HarderTC (2010) Increasing Prevalence of Unique Mutation Patterns in H5N1 Avian Influenza Virus HA and NA Glycoproteins from Human Infections in Egypt. Sequencing doi: 10.1155/2010/450823.
31. Yong E (2012) Mutations behind flu spread revealed. Nature. Available: http://www.nature.com/news/mutations-behind-flu-spread-revealed-1.10394.
32. Imai M, (2012) KawaokaY (2012) The role of receptor binding specificity in interspecies transmission of influenza viruses. Curr Opin Virol 2: 1-8.
33. Chen LM, Blixt O, Stevens J, Lipatov AS, Davis CT, et al. (2012) In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity. Virology 422: 105-113.
34. Yamada S, Suzuki Y, Suzuki T, Le MQ, Nidom CA, et al. (2006) Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors. Nature 444: 378-382.
35. Chutinimitkul S, van Riel D, Munster VJ, van den Brand JMA, Rimmelzwaan GF, et al. (2010) In Vitro assessment of attachment pattern and replication efficiency of H5N1 influenza A viruses with altered receptor specificity. J Virol 84: 6825-6833.
36. Maines TR, Chen LM, van Hoeven N, Tumpey TM, Blixt O, et al. (2011) Effect of receptor binding domain mutations on receptor binding and transmissibility of avian influenza H5N1 viruses. Virology 413: 139-147.
37. Su Y, Yang HY, Zhang BJ, Jiao HL, Tien P, (2008) Analysis of a point mutation in H5N1 avian influenza virus hemagglutinin in relation to virus entry into live mammalian cells. Arch Virol 153: 2253-2261.
38. Lycet SJ, Ward MJ, Lewis FI, Poon AFY, Pond SLK, et al. (2009) Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data. J Virol 83: 9901-9910.
39. Garcia JM, Pepin S, Lagarde N, Ma ESK, Vogel FR, et al. (2009) Heterosubtype neutralizing responses to influenza A (H5N1) viruses are mediated by antibodies to virus haemagglutinin. PLoS Med. 6: e1000049.
40. Hu H, Voss J, Zhang G, Buchy P, Zuo T, et al. (2012) A human antibody recognizing a conserved epitope of H5 hemagglutinin broadly neutralizes highly pathogenic avian influenza H5N1 viruses. J. Virol. 86: 2978-2989.
41. Cao Z, Meng J, LiX, Wu R, Huang Y, et al. (2012) The epitope and neutralization mechanism of AVFluIgG01, a broad-reactive human monoclonal antibody against H5N1 influenza virus. PloS ONE 7: e38126.
42. World Health Organization (WHO) website. Availability of a new recombinant A(H5N1) candidate vaccine virus IDCDC-RG-29 (clade 2.2.1). Available: http://www.who.int/influenza/vaccines/virus/h5n1virus_september/en/. Published 2011 September 6. Accessed 2012 Nov 3.
43. Cattoli G, Monne I, Fusaro A, Joannis TM, Lombin LH, et al. (2009) Highly pathogenic avian influenza virus subtype H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates. PLoS One 4: ID e4842.
44. Arafa AM, Suarez DL, Hassan MK, Aly MM (2010) Phylogenetic analysis of HA and NA genes of HPAI-H5N1 Egyptian strains isolated from 2006 to 2008 indicates heterogeneity with multiple distinct sublineages. Avian Diseases 51: supplement 1, 345-349.
45. Abdel-Moneim AS, Afifi MA, El-Kady MF, (2011) Genetic drift evolution under vaccination pressure among H5N1 Egyptian. Virol J 8: 283-290.
46. Saad MD, Ahmed LS, Gamal-Eldein MA, Fouda MK, Khalil F, et al. (2007) Possible avian influenza (H5N1) from migratory bird, Egypt. Emerg Infect Dis 13: 1120-1121.