Phylodynamics and molecular evolution of influenza A virus nucleoprotein genes in Taiwan between 1979 and 2009

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Lin, Jih Hui ^a,b   Chiu, Shu Chun ^a,c   Cheng, Ju Chien ^d   Chang, Hui Wen ^a   Hsiao, Kuang Liang ^b   Lin, Yung Cheng ^b   Wu, Ho Sheng ^a   Salemi, Marco ^e   Liu, Hsin Fu ^b,c,f  

^a CENTER FOR DISEASE CONTROL   (Taiwan)

^b NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

^c NATIONAL YANG MING UNIVERSITY   (Taiwan)

^d CHINA MEDICAL UNIVERSITY   (Taiwan)

^e UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^f MACKAY MEMORIAL HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLADISTICS; CODON; CONTROLLED STUDY; GENE ISOLATION; GENETIC SELECTION; GENETIC VARIABILITY; HOST RANGE; INFECTION RATE; INFLUENZA VIRUS A; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOPROTEIN GENE; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEQUENCE HOMOLOGY; TAIWAN; VIRUS GENE; VIRUS TRANSMISSION; ANIMAL; AVIAN INFLUENZA; BAYES THEOREM; BIRD; CLASSIFICATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; INFLUENZA; MONTE CARLO METHOD; ORTHOMYXOVIRUS INFECTION; PHYLOGENY; POPULATION DYNAMICS; PROBABILITY; SPECIES DIFFERENCE; SWINE; SWINE DISEASE; TIME; VIROLOGY;

AVES; HUMAN INFLUENZA VIRUS; INFLUENZA A VIRUS; SUIDAE;

CORE PROTEIN; NP PROTEIN, INFLUENZA A VIRUS; RNA BINDING PROTEIN;

ANIMALS; BAYES THEOREM; BIRDS; EVOLUTION, MOLECULAR; GENETIC VARIATION; HUMANS; INFLUENZA A VIRUS; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MARKOV CHAINS; MONTE CARLO METHOD; ORTHOMYXOVIRIDAE INFECTIONS; PHYLOGENY; POPULATION DYNAMICS; RNA-BINDING PROTEINS; SPECIES SPECIFICITY; SWINE; SWINE DISEASES; TAIWAN; TIME FACTORS; VIRAL CORE PROTEINS;

EID: 80051634063     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023454     Document Type: Article

References (49)

1. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, et al. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453: 615-619.
2. Pybus OG, Rambaut A, (2009) Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet 10: 540-550.
3. Gammelin M, Altmuller A, Reinhardt U, Mandler J, Harley VR, et al. (1990) Phylogenetic analysis of nucleoproteins suggests that human influenza A viruses emerged from a 19th-century avian ancestor. Mol Biol Evol 7: 194-200.
4. Gorman OT, Donis RO, Kawaoka Y, Webster RG, (1990) Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus. J Virol 64: 4893-4902.
5. Kida H, Shortridge KF, Webster RG, (1988) Origin of the hemagglutinin gene of H3N2 influenza viruses from pigs in China. Virology 162: 160-166.
6. Lamb RA, (1989) The genes and proteins of the influenza viruses. In: Krug RM, editors. The influenza viruses Plenum Publish Corp. New York pp. 1-87.
7. Nakajima K, Desselberger U, Palese P, (1978) Recent human influenza A (H1N1) viruses are closely related genetically to strains isolated in 1950. Nature 274: 334-339.
8. Drummond AJ, Rambaut A, Shapiro B, Pybus OG, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22: 1185-1192.
9. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, et al. (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science 320: 340-346.
10. Lin JH, Chiu SC, Cheng JC, Chang HW, Hsiao KL, et al. (2011) Molecular epidemiology and antigenic analyses of influenza A viruses H3N2 in Taiwan. Clin Microbiol Infect 17: 214-222.
11. Portela A, Digard P, (2002) The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication. J Gen Virol 83: 723-734.
12. Fu TM, Friedman A, Ulmer JB, Liu MA, Donnelly JJ, (1997) Protective cellular immunity: cytotoxic T-lymphocyte responses against dominant and recessive epitopes of influenza virus nucleoprotein induced by DNA immunization. J Virol 71: 2715-2721.
13. Kreijtz JH, de Mutsert G, van Baalen CA, Fouchier RA, Osterhaus AD, et al. (2008) Cross-recognition of avian H5N1 influenza virus by human cytotoxic T-lymphocyte populations directed to human influenza A virus. J Virol 82: 5161-5166.
14. Neumann G, Castrucci MR, Kawaoka Y, (1997) Nuclear import and export of influenza virus nucleoprotein. J Virol 71: 9690-9700.
15. Rimmelzwaan GF, Boon AC, Voeten JT, Berkhoff EG, Fouchier RA, et al. (2004) Sequence variation in the influenza A virus nucleoprotein associated with escape from cytotoxic T lymphocytes. Virus Res 103: 97-100.
16. Voeten JT, Bestebroer TM, Nieuwkoop NJ, Fouchier RA, Osterhaus AD, et al. (2000) Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes. J Virol 74: 6800-6807.
17. Townsend AR, Skehel JJ, (1984) The influenza A virus nucleoprotein gene controls the induction of both subtype specific and cross-reactive cytotoxic T cells. J Exp Med 160: 552-563.
18. Yewdell JW, Bennink JR, Smith GL, Moss B, (1985) Influenza A virus nucleoprotein is a major target antigen for cross-reactive anti-influenza A virus cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 82: 1785-1789.
19. Minin VN, Bloomquist EW, Suchard MA, (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25: 1459-1471.
20. Chen GW, Chang SC, Mok CK, Lo YL, Kung YN, et al. (2006) Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis 12: 1353-1360.
21. Suzuki Y, (2006) Natural selection on the influenza virus genome. Mol Biol Evol 23: 1902-1911.
22. Andersen MH, Sondergaard I, Zeuthen J, Elliott T, Haurum JS, (1999) An assay for peptide binding to HLA-Cw*0102. Tissue Antigens 54: 185-190.
23. Gianfrani C, Oseroff C, Sidney J, Chesnut RW, Sette A, (2000) Human memory CTL response specific for influenza A virus is broad and multispecific. Hum Immunol 61: 438-452.
24. Scholtissek C, Burger H, Kistner O, Shortridge KF, (1985) The nucleoprotein as a possible major factor in determining host specificity of influenza H3N2 viruses. Virology 147: 287-294.
25. Reid AH, Fanning TG, Janczewski TA, Lourens RM, Taubenberger JK, (2004) Novel origin of the 1918 pandemic influenza virus nucleoprotein gene. J Virol 78: 12462-12470.
26. Varich NL, Sadykova GK, Prilipov AG, Kochergin-Nikitsky KS, Kushch AA, et al. (2011) Antibody-binding epitope differences in the nucleoprotein of avian and Mammalian influenza a viruses. Viral Immunol 24: 101-107.
27. Hinshaw VS, Webster RG, (1982) The natural history of influenza A viruses. In: Beare AS, editors. Basic and Applied Influenza Research Boca Raton, FL, CRC Press pp. 79-104.
28. Kawaoka Y, Chambers TM, Sladen WL, Webster RG, (1988) Is the gene pool of influenza viruses in shorebirds and gulls different from that in wild ducks? Virology 163: 247-250.
29. Kilbourne ED, (2006) Influenza pandemics of the 20th century. Emerg Infect Dis 12: 9-14.
30. Smith GJ, Bahl J, Vijaykrishna D, Zhang J, Poon LL, et al. (2009) Dating the emergence of pandemic influenza viruses. Proc Natl Acad Sci U S A 106: 11709-11712.
31. Kingman JFC, (1982) The Coalescent Stoch Proc Appl 13: 235-248.
32. Felsenstein J, (2005) Using the quantitative genetic threshold model for inferences between and within species. Philos Trans R Soc Lond B Biol Sci 360: 1427-1434.
33. Shapiro B, Rambaut A, Drummond AJ, (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol 23: 7-9.
34. Felsenstein J, (2006) Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol 23: 691-700.
35. Pybus OG, Rambaut A, Harvey PH, (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437.
36. Strimmer K, Pybus OG, (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 18: 2298-2305.
37. Lemey P, Salemi M, Vandamme AM, eds. (2009) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. New York Cambridge University Press.
38. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, et al. (2009) Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197-201.
39. Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459: 1122-1125.
40. Shih AC, Lee DT, Peng CL, Wu YW, (2007) Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences. BMC Bioinformatics 8: 63.
41. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
42. Posada D, (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
43. Hasegawa M, Kishino H, Yano T, (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
44. Wilgenbusch JC, Swofford D, (2003) Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics Chapter 6.
45. Rodrigo AG, Felsenstein J, (1999) Coalescent approaches to HIV population genetics. In: Crandall KA, editors. The evolution of HIV Baltimore (Md) Johns Hopkins University Press pp. 233-272.
46. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
47. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
48. Drummond AJ, Ho SY, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88.
49. Pond SL, Frost SD, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.