The variable codons of H5N1 avian influenza A virus haemagglutinin genes

Science in China, Series C: Life Sciences

Volumn 51, Issue 11, 2008, Pages 987-993

  Shi, WeiFeng ^a   Gibbs, Mark J ^b   Zhang, YanZhou ^c   Zhuang, DongMing ^a   Dun, AiShe ^a   Yu, GuangFu ^a   Yang, NaNa ^a   Murphy, Robert W ^d   Zhu, ChaoDong ^c  

^a SHANDONG PROVINCIAL HOSPITAL AFFILIATED TO SHANDONG FIRST MEDICAL UNIVERSITY   (China)

^b AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^c INSTITUTE OF ZOOLOGY   (China)

^d DEPARTMENT OF NATURAL HISTORY   (Canada)

Author keywords

Avian influenza virus; Codon; H5N1; HA; Positive selection pressure

Indexed keywords

INFLUENZA VIRUS HEMAGGLUTININ;

ANIMAL; ARTICLE; AVIAN INFLUENZA; BIOLOGICAL MODEL; BIRD; CODON; GENETIC DATABASE; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; HUMAN; INFLUENZA; INFLUENZA VIRUS A H5N1; ISOLATION AND PURIFICATION; MAMMAL; ORTHOMYXOVIRUS INFECTION; SPECIES DIFFERENCE; STATISTICAL MODEL; VIROLOGY; VIRUS GENE;

ANIMALS; BIRDS; CODON; DATABASES, GENETIC; GENES, VIRAL; GENETIC VARIATION; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; LIKELIHOOD FUNCTIONS; MAMMALS; MODELS, GENETIC; ORTHOMYXOVIRIDAE INFECTIONS; SELECTION (GENETICS); SPECIES SPECIFICITY;

AVES; AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS; INFLUENZAVIRUS A; ORTHOMYXOVIRIDAE;

EID: 55949134966     PISSN: 10069305     EISSN: 18622798     Source Type: Journal    
DOI: 10.1007/s11427-008-0131-8     Document Type: Article

References (28)

1. R. M. Bush W. M. Fitch C. A. Bender 1999 Positive selection on the H3 hemagglutinin gene of human influenza virus A Mol Biol Evol 16 1457 1465
2. R. G. Webster W. J. Bean O. T. Gorman 1992 Evolution and ecology of influenza A viruses Microbiol Rev 56 152 179
3. S. Yamada Y. Suzuki T. Suzuki 2006 Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors Nature 444 378 382
4. W. M. Fitch J. M. E. Leiter X. Li 1991 Positive Darwinian evolution in human influenza A viruses Proc Natl Acad Sci USA 88 4270 4274
5. Y. Ina T. Gojobori 1994 Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses Proc Natl Acad Sci USA 91 8388 8392
6. L. Campitelli M. Ciccozzi M. Salemi 2006 H5N1 influenza virus evolution: a comparison of different epidemics in birds and humans (1997-2004) J Gen Virol 87 955 960
7. G. J. Smith T. S. P. Naipospos T. D. Nguyen 2006 Evolution and adaptation of H5N1 influenza virus in avian and human hosts in Indonesia and Vietnam Virology 350 258 268
8. M. Ciccozzi S. Montieri M. Facchini 2007 Evolutionary analysis of HA and NS1 genes of H5N1 influenza viruses in 2004-2005 epidemics Avian Dis 51 1Suppl 455 460
9. R. Nielsen 2002 Mapping mutations on phylogenies Syst Biol 51 5 729 739
10. Y. Suzuki T. Gojobori 1999 A method for detecting positive selection at single amino acid sites Mol Biol Evol 16 1315 1328
11. J. P. Huelsenbeck K. A. Dyer 2004 Bayesian estimation of positively selected sites J Mol Evol 58 661 672
12. R. Nielsen Z. H. Yang 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene Genetics 148 929 936
13. Z. H. Yang R. Nielsen N. Goldman 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 431 449
14. S. L. Kosakovsky Pond S. D. W. Frost 2005 Not so different after all: A comparison of methods for detecting amino acid sites under selection Mol Biol and Evol 22 1208 1222
15. Y. Suzuki 2004 New methods for detecting positive selection at single amino acid sites J Mol Evol 59 11 19
16. Z. Yang W. Swanson 2002 Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes Mol Biol Evol 19 1 49 57
17. S. L. Kosakovsky Pond S. D. W. Frost 2005 Datamonkey: rapid detection of selective pressure on individual sites of codon alignments Bioinformatics 21 10 2531 2533
18. J. D. Thompson T. J. Gibson F. Plewniak 1997 The CLUSTAL_X windows interface: Flexible strategies for multiple sequence align ment aided by quality analysis tools Nucl Acids Res 25 4876 4882
19. S. Guindon O. Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704
20. S. L. Kosakovsky Pond S. D. W. Frost S. V. Muse 2005 HyPhy: hypothesis testing using phylogenies Bioinformatics 21 676 679
21. M. Hasegawa H. Kishino T. A. Yano 1985 Dating of the human ape splitting by a molecular clock of mitochondrial-DNA J Mol Evol 22 160 174
22. S. V. Muse B. S. Gaut 1994 A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome Mol Biol Evol 11 715 724
23. D. Normile 2006 Avian influenza: Evidence points to migratory birds in H5N1 spread Science 311 1225
24. R. Webby E. Hoffmann R. Webster 2006 Molecular constrains to interspecies transmission of viral pathogens Nature Med 10 S77 S81
25. N. V. Kaverin I. A. Rudneva N. A. Ilyushina 2002 Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants J Gen Virol 83 2497 2505
26. A. Gambaryan S. Yamnikova D. Lvov 2005 Receptor specificity of influenza viruses from birds and mammals: New data on involvement of the inner fragments of the carbohydrate chain Virology 334 276 283
27. N. A. Ilyushina I. A. Rudneva A. S. Gambaryan 2004 Receptor specificity of H5 influenza virus escapemutants Virus Res 100 237 241
28. R. G. Wallace H. HoDac R. H. Lathrop 2007 A statistical phylogeography of influenza A H5N1 Proc Natl Acad Sci USA 104 4473 4478