Prediction of possible mutations in H5N1 hemagglutitins of influenza A virus by means of logistic regression

Comparative Clinical Pathology

Volumn 15, Issue 4, 2006, Pages 255-261

  Wu, Guang ^a   Yan, Shaomin ^a  

^a DreamSciTech Consulting   (China)

Author keywords

Hemagglutinin; Influenza; Logistic regression; Mutation; Prediction

Indexed keywords

AMINO ACID; INFLUENZA VIRUS HEMAGGLUTININ; RNA;

ARTICLE; CODON; CONTROLLED STUDY; GENE MUTATION; INFLUENZA VIRUS A; LOGISTIC REGRESSION ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; POPULATION RESEARCH; PREDICTION; PROBABILITY; RNA SEQUENCE; RNA TRANSLATION;

EID: 33751086728     PISSN: 16185641     EISSN: 1618565X     Source Type: Journal    
DOI: 10.1007/s00580-006-0638-y     Document Type: Article

References (74)

1. Abbottbase (1992) Pharmacokinetic System Operations Manual. version 1.10. Abbott Laboratories, Abbott Park, IL, 6, pp 45-62
2. Baigent SJ, Mccauley JW (2003) Influenza type A in humans, mammals and birds: Determinants of virus virulence, host-range and interspecies transmission. Bioessays 25:657-671
3. Bean WJ, Schell M, Katz J, Kawaoka Y, Naeve C, Gorman O, Webster RG (1992) Evolution of the H3 influenza virus hemagglutinin from human and nonhuman hosts. J Virol 66:1129-1138
4. De La Barrera CA, Reyes-Teran G (2005) Influenza: Forecast for a pandemic. Arch Med Res 36:628-636
5. Donis RO, Bean WJ, Kawaoka Y, Webster RG (1989) Distinct lineages of influenza virus H4 hemagglutinin genes in different regions of the world. Virology 169:408-417
6. Draper NR, Smith H (1981) Applied regression analysis, 2nd edn. Wiley, New York
7. Feller W (1968) An introduction to probability theory and its applications. 3rd ed. Vol, I. Wiley, New York
8. Fitch WM, Bush RM, Bender CA, Cox NJ (1997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci USA 94:7712-7718
9. Gao N, Yan S, Wu G (2006) Pattern of positions sensitive to mutations in human haemoglobin α-chain. Protein Pept Lett 13:101-107
10. Guan Y, Poon LL, Cheung CY, Ellis TM, Lim W, Lipatov AS, Chan KH, Sturm-Ramirez KM, Cheung CL, Leung YH, Yuen KY, Webster RG, Peiris JS (2004) H5N1 influenza: A protean pandemic threat. Proc Natl Acad Sci USA 101:8156-8161
11. Healy MJR (1979) Outliers in clinical chemistry quality-control schemes. Clin Chem 25:675-677
12. Hoffmann E, Stech J, Leneva I, Krauss S, Scholtissek C, Chin PS, Peiris M, Shortridge KF, Webster RG (2000) Characterization of the influenza A virus gene pool in avian species in southern China: Was H6N1 a derivative or a precursor of H5N1? Virology 74:6309-6315
13. Hosmer DW Jr, Lemeshow S (2000) Applied logistic regression, 2nd edn. Wiley, New York
14. Katz JM (2003) The impact of avian influenza viruses on public health. Avian Dis 47:914-920
15. Kawaoka Y, Yamnikova S, Chambers TM, Lvov DK, Webster RG (1990) Molecular characterization of a new hemagglutinin, subtype H14, of influenza A virus. Virology 179:759-767
16. Krauss S, Walker D, Pryor SP, Niles L, Chenghong L, Hinshaw VS, Webster RG (2004) Influenza A viruses of migrating wild aquatic birds in North America. Vector Borne Zoonotic Dis 4:177-189
17. Li KS, Guan Y, Wang J, Smith GJ, Xu KM, Duan L, Rahardjo AP, Puthavathana P, Buranathai C, Nguyen TD, Estoepangestie AT, Chaisingh A, Auewarakul P, Long HT, Hanh NT, Webby RJ, Poon LL, Chen H, Shortridge KF, Yuen KY, Webster RG, Peiris JS (2004) Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430:209-213
18. Lin YP, Shaw M, Gregory V, Cameron K, Lim W, Klimov A, Subbarao K, Guan Y, Krauss S, Shortridge K, Webster R, Cox N, Hay A (2000) Avian-to-human transmission of H9N2 subtype influenza A viruses, relationship between H9N2 and H5N1 human isolates. Proc Natl Acad Sci USA 97:9654-9658
19. Miller WG (2006) OpenStat4, Version 13, Release 3, http://www.statpages.org/miller/openstat
20. Nobusawa E, Aoyama T, Kato H, Suzuki Y, Tateno Y, Nakajima K (1991) Comparison of complete amino acid sequences and receptor-binding properties among 13 serotypes of hemagglutinins of influenza A viruses. Virology 182:475-485
21. Perdue ML, Swayne DE (2005) Public health risk from avian influenza viruses. Avian Dis 49:317-327
22. Reid AH, Taubenberger JK (2003) The origin of the 1918 pandemic influenza virus: A continuing enigma. J Gen Virol 84:2285-2292
23. Rohm C, Horimoto T, Kawaoka Y, Suss J, Webster RG (1995) Do hemagglutinin genes of highly pathogenic avian influenza viruses constitute unique phylogenetic lineages? Virology 209:664-670
24. Schafer JR, Kawaoka Y, Bean WJ, Suss J, Senne D, Webster RG (1993) Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology 194:781-788
25. The Lancet Infectious Diseases (2006) Lancet Infect Dis 6:315
26. Tognotti E (2003) Scientific triumphalism and learning from facts: bacteriology and the "Spanish flu" challenge of 1918. Soc Hist Med 16:97-110
27. 2 affinity. Comp Haematol Int 9:148-151
28. Wu G (2000a) Frequency and Markov chain analysis of amino-acid sequence of human glutathione reductase. Biochem Biophys Res Commun 268:823-826
29. Wu G (2000b) Frequency and Markov chain analysis of amino-acid sequence of human tumor necrosis factor. Cancer Lett 153:145-150
30. Wu G (2000c) Frequency and Markov chain analysis of amino-acid sequences of mouse p53. Hum Exp Toxicol 19:535-539
31. Wu G (2000d) Frequency and Markov chain analysis of the amino acid sequence of human alcohol dehydrogenase α-chain. Alcohol Alcohol 35:302-306
32. Wu G (2000e) Frequency and Markov chain analysis of the amino-acid sequence of sheep p53 protein. J Biochem Mol Biol Biophys 4:179-185
33. Wu G (2000f) The first, second and third order Markov chain analysis on amino acids sequence of human tyrosine aminotransferase and its variant causing tyrosinemia type II. Pediatr Relat Top 39:37-47
34. Wu G (2000g) The first, second, third and fourth order Markov chain analysis on amino acids sequence of human dopamine β-hydroxylase. Mol Psychiatry 5:448-451
35. Wu G, Yan S (2000a) Frequency and Markov chain analysis of amino-acids sequence of human platelet-activating factor acetylhydrolase αα-subunit and its variant causing the lissencephaly syndrome. Pediatr Relat Top 39:513-526
36. Wu G, Yan S (2000b) Prediction of distributions of amino acids and amino acid pairs in human haemoglobin α-chain and its seven variants causing αα-thalassemia from their occurrences according to the random mechanism. Comp Haematol Int 10:80-84
37. Wu G, Yan S (2000c) Prediction of two- and three-amino acid sequence of human acute myeloid leukemia 1 protein from its amino acid composition. Comp Haematol Int 10:85-89
38. Wu G, Yan S (2000d) Prediction of two- and three-amino-acid sequences of Citrobacter freundii β-lactamase from its amino acid composition. J Mol Microbiol Biotechnol 2:277-281
39. Wu G, Yan S (2001a) Frequency and Markov chain analysis of amino-acid sequences of human connective tissue growth factor. J Mol Model 5:120-124
40. Wu G, Yan S (2001b) Prediction of presence and absence of two- and three-amino-acid sequence of human monoamine oxidase B from its amino acid composition according to the random mechanism. Biomol Eng 18:23-27
41. Wu G, Yan S (2001c) Prediction of presence and absence of two- and three-amino-acid sequence of human tyrosinase from their amino acid composition and related changes in human tyrosinase variant causing oculocutaneous albinism. Pediatr Relat Top 40:153-166
42. Wu G, Yan S (2001d) Analysis of distributions of amino acids, amino acid pairs and triplets in human insulin precursor and four variants from their occurrences according to the random mechanism. J Biochem Mol Biol Biophys 5:293-300
43. Wu G, Yan S (2001e) Analysis of distributions of amino acids and amino acid pairs in human tumor necrosis factor precursor and its eight variants according to random mechanism. J Mol Model 7:318-323
44. Wu G, Yan S (2002a) Determination of amino acid pairs sensitive to variants in human low-density lipoprotein receptor precursor by means of a random approach. J Biochem Mol Biol Biophys 6:401-406
45. Wu G, Yan S (2002b) Estimation of amino acid pairs sensitive to variants in human phenylalanine hydroxylase protein by means of a random approach. Peptides 23:2085-2090
46. Wu G, Yan S (2002c) Random analysis of presence and absence of two- and three-amino-acid sequences and distributions of amino acids, two- and three-amino-acid sequences in bovine p53 protein. Mol Biol Today 3:31-37
47. Wu G, Yan S (2002d) Analysis of distributions of amino acids in the primary structure of apoptosis regulator Bcl-2 family according to the random mechanism. J Biochem Mol Biol Biophys 6:407-414
48. Wu G, Yan S (2002e) Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family according to the random mechanism. J Mol Model 8:191-198
49. Wu G, Yan S (2002f) Randomness in the primary structure of protein: methods and implications. Mol Biol Today 3:55-69
50. Wu G, Yan S (2003a) Analysis of amino acid pairs sensitive to variants in human collagen αα5(IV) chain precursor by means of a random approach. Peptides 24:347-352
51. Wu G, Yan S (2003b) Determination of amino acid pairs in human haemoglobulin αα-chain sensitive to variants by means of a random approach. Comp Clin Path 12:21-25
52. Wu G, Yan S (2003c) Determination of amino acid pairs in human p53 protein sensitive to mutations/variants by means of a random approach. J Mol Model 9:337-341
53. Wu G, Yan S (2003d) Determination of amino acid pairs in Von Hippel-Lindau disease tumour suppressor (G7 protein) sensitive to variants by means of a random approach. J Appl Res 3:512-520
54. Wu G, Yan S (2003e) Determination of amino acid pairs sensitive to variants in human β-glucocerebrosidase by means of a random approach. Protein Eng 16:195-199
55. Wu G, Yan S (2003f) Determination of amino acid pairs sensitive to variants in human Bruton's tyrosine kinase by means of a random approach. Mol Simul 29:249-254
56. Wu G, Yan S (2003g) Determination of amino acid pairs sensitive to variants in human coagulation factor IX precursor by means of a random approach. J Biomed Sci 10:451-454
57. Wu G, Yan S (2003h) Prediction of amino acid pairs sensitive to mutations in the spike protein from SARS related coronavirus. Peptides 24:1837-1845
58. Wu G, Yan S (2004a) Amino acid pairs sensitive to variants in human collagen α1(I) chain precursor. EXCLI J 3:10-19
59. Wu G, Yan S (2004b) Determination of amino acid pairs sensitive to variants in human copper-transporting ATPase 2. Biochem Biophys Res Commun 319:27-31
60. Wu G, Yan S (2004c) Fate of 130 hemagglutinins from different influenza A viruses. Biochem Biophys Res Commun 317:917-924
61. Wu G, Yan S (2004d) Potential targets for anti-SARS drugs in the structural proteins from SARS related coronavirus. Peptides 25:901-908
62. Wu G, Yan S (2004e) Susceptible amino acid pairs in variants of human collagen α1(III) chain precursor. EXCLI J 3:20-28
63. Wu G, Yan S (2004f) Determination of sensitive positions to mutations in human p53 protein. Biochem Biophys Res Commun 321:313-319
64. Wu G, Yan S (2005a) Amino acid pairs susceptible to variants in human protein C precursor. Protein Pept Lett 10:491-494
65. Wu G, Yan S (2005b) Mutation features of 215 polymerase proteins from different influenza A viruses. Med Sci Monit 11:BR367-BR372
66. Wu G, Yan S (2005c) Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species. J Mol Model 11:8-16
67. Wu G, Yan S (2005d) Timing of mutation in hemagglutinins from influenza A virus by means of unpredictable portion of amino-acid pair and fast Fourier transform. Biochem Biophys Res Commun 333:70-78
68. Wu G, Yan S (2005e) Searching of main cause leading to severe influenza A virus mutations and consequently to influenza pandemics/epidemics. Amer J Infect Dis 1:116-123
69. Wu G, Yan S (2005f) Prediction of mutation trend in hemagglutinins and neuraminidases from influenza A viruses by means of cross-impact analysis. Biochem Biophys Res Commun 326:475-482
70. Wu G, Yan S (2005g) Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids. Biochem Biophys Res Commun 337:692-700
71. Wu G, Yan S (2006a) Fate of influenza A virus proteins. Protein Pept Lett 13:377-384
72. Wu G, Yan S (2006b) Mutation trend of hemagglutinin of influenza A virus: A review from computational mutation viewpoint. Acta Pharmacol Sin 27:513-526
73. Wu G, Yan S (2006c) Timing of mutation in hemagglutinins from influenza A virus by means of amino-acid distribution rank and fast Fourier transform. Protein Pept Lett 13:143-148
74. Wu G, Yan S (2006d) Determination of mutation trend in hemagglutinins by means of translation probability between RNA codons and mutated amino acids. Protein Pept Lett 13:601-609