Evolutionary dynamics of Newcastle disease virus

Virology

Volumn 391, Issue 1, 2009, Pages 64-72

  Miller, Patti J ^a   Kim, L Mia ^a   Ip, Hon S ^b   Afonso, Claudio L ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b NATIONAL WILDLIFE HEALTH CENTER   (United States)

Author keywords

APMV 1; Evolution; Newcastle disease virus; Recombination; Selection; Virulence

Indexed keywords

HYBRID PROTEIN; VIRUS PROTEIN;

ARTICLE; BIRD; CONTROLLED STUDY; FUSION GENE; GENETIC RECOMBINATION; GENOMICS; GENOTYPE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NEWCASTLE DISEASE PARAMYXOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CLEAVAGE; VIRUS GENOME; VIRUS MUTATION; VIRUS VIRULENCE; WILD ANIMAL;

EVOLUTION, MOLECULAR; GENOME, VIRAL; NEWCASTLE DISEASE VIRUS; PHYLOGENY; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; VIRAL FUSION PROTEINS; VIRULENCE;

AVES; NEWCASTLE DISEASE VIRUS;

EID: 67650725425     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2009.05.033     Document Type: Article

References (51)

1. Afonso C.L. Not so fast on recombination analysis of Newcastle disease virus. J. Virol. 82 18 (2008) 9303
2. Alexander D.J., Campbell G., Manvell R.J., Collins M.S., Parsons G., and McNulty M.S. Characterisation of an antigenically unusual virus responsible for two outbreaks of Newcastle disease in the Republic of Ireland in 1990. Vet. Rec. 130 4 (1992) 65-68
3. Alexander D.J., Gough R.E., Saif Y.M., Barnes H.J., Glisson J.R., Fadly A.M., McDougald L.R., and Swayne D.E. Newcastle disease, other avian Paramyxoviruses, and Pneumovirus infections. Disease of Poultry vol. 11th (2003), Iowa State Press, Ames, IA 63-92
4. Anisimova M., Nielsen R., and Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164 3 (2003) 1229-1236
5. Boni M.F., Posada D., and Feldman M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176 2 (2007) 1035-1047
6. Bush, R.M., (2001). Predicting adaptive evolution 2(5), 387-392.
7. Chare E.R., Gould E.A., and Holmes E.C. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 84 Pt 10 (2003) 2691-2703
8. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
9. Duarte E.A., Novella I.S., Weaver S.C., Domingo E., Wain-Hobson S., Clarke D.K., Moya A., Elena S.F., de la Torre J.C., and Holland J.J. RNA virus quasispecies: significance for viral disease and epidemiology. Infect. Agents. Dis. 3 4 (1994) 201-214
10. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nuclei. Acids Res. 32 5 (2004) 1792-1797
11. Gibbs M.J., Armstrong J.S., and Gibbs A.J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16 7 (2000) 573-582
12. Glickman R.L., Syddall R.J., Iorio R.M., Sheehan J.P., and Bratt M.A. Quantitative basic residue requirements in the cleavage-activation site of the fusion glycoprotein as a determinant of virulence for Newcastle disease virus. J. Virol. 62 1 (1988) 354-356
13. Gould A.R., Kattenbelt J.A., Selleck P., Hansson E., la-Porta A., and Westbury H.A. Virulent Newcastle disease in Australia: molecular epidemiological analysis of viruses isolated prior to and during the outbreaks of 1998-2000. Virus Res. 77 1 (2001) 51-60
14. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 5 (2003) 696-704
15. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. 41 (1999) 95-98
16. Han G.Z., He C.Q., Ding N.Z., and Ma L.Y. Identification of a natural multi-recombinant of Newcastle disease virus. Virology 371 1 (2008) 54-60
17. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 2 (1985) 160-174
18. Huson D.H., and Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23 2 (2006) 254-267
19. Islam M.A., Ito T., Takakuwa H., Takada A., Itakura C., and Kida H. Acquisition of pathogenicity of a Newcastle disease virus isolated from a Japanese quail by intracerebral passage in chickens. Jpn. J. Vet. Res 42 3-4 (1994) 147-156
20. Kim L.M., Suarez D.L., and Afonso C.L. Biotechnologia e Saude Animal (2006), Viscosa, Brazil
21. Kim L.M., King D.J., Curry P.E., Suarez D.L., Swayne D.E., Stallknecht D.E., Slemons R.D., Pedersen J.C., Senne D.A., Winker K., and Afonso C.L. phylogenetic diversity among low virulence Newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to poultry-origin isolates. J. Virol. 81 22 (2007) 12641-12653
22. Kosiol C., Bofkin L., and Whelan S. Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. J. Biomed. Informatics 39 1 (2006) 51-61
23. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 2 (2004) 150-163
24. Lai M.M. RNA recombination in animal and plant viruses. Microbiol. Rev. 56 1 (1992) 61-79
25. Martin D.P., Williamson C., and Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21 2 (2005) 260-262
26. Maynard Smith J. Analyzing the mosaic structure of genes. J. Mol. Evol. 35 (1992) 126-129
27. Morrison T.G. Structure and function of a paramyxovirus fusion protein. Biochim. Biophys. Acta 1614 1 (2003) 73-84
28. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 5 (1986) 418-426
29. OIE, B.S.C. Manual of Diagnostic Tests and Vaccines for Terrestrial Animals: Mammals, Birds and Bees. 5 ed. (2004), Office international des âepizooties, Paris Chapter 2.1.15. 2 vols.
30. Ota T., and Nei M. Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol. Biol. Evol. 11 4 (1994) 613-619
31. Perozo F., Merino R., Afonso C.L., Villegas P., and Calderon N. Biological and phylogenetic characterization of virulent Newcastle disease virus circulating in Mexico. Avian. Dis. 52 3 (2008) 472-479
32. Plemper R.K., and Compans R.W. Mutations in the putative HR-C region of the measles virus F2 glycoprotein modulate syncytium formation. J. Virol. 77 7 (2003) 4181-4190
33. Pond S.L., Frost S.D., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 5 (2005) 676-679
34. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 9 (1998) 817-818
35. Posada D., and Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. PNAS 98 (2001) 13757-13762
36. Qin Z., Sun L., Ma B., Cui Z., Zhu Y., Kitamura Y., and Liu W. F gene recombination between genotype II and VII Newcastle disease virus. Virus Res. 131 2 (2008) 299-303
37. Qin Z.M., Tan L.T., Xu H.Y., Ma B.C., Wang Y.L., Yuan X.Y., and Liu W.J. Pathotypical characterization and molecular epidemiology of Newcastle disease virus isolates from different hosts in China from 1996 to 2005. J. Clin. Microbiol. 46 2 (2008) 601-611
38. Rambaut A., and Drummond A.J. Tracer (2007). http://beast.bio.ed.ac.uk/Tracer http://beast.bio.ed.ac.uk/Tracer
39. Rodriguez F., Oliver J.F., Marin A., and Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485-501
40. Rott R. Molecular basis of infectivity and pathogenicity of Myxovirus. Arch. Virol. 59 (1979) 285-298
41. Salminen M.O., Carr J.K., Burke D.S., and McCutchan F.E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 11 (1995) 1423-1425
42. Sawyer S.A. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6 (1989) 526-538
43. Spann K.M., Collins P.L., and Teng M.N. Genetic recombination during coinfection of two mutants of human respiratory syncytial virus. J. Virol. 77 20 (2003) 11201-11211
44. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 22 (1994) 4673-4680
45. Worobey M., and Holmes E.C. Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol. 80 Pt 10 (1999) 2535-2543
46. Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51 5 (2000) 423-432
47. Yang Z., and Bielawski J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15 12 (2000) 496-503
48. Yang Z., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 6 (2002) 908-917
49. Yang Z., and Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19 1 (2002) 49-57
50. Yang Z., Nielsen R., Goldman N., and Pedersen A.M. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 1 (2000) 431-449
51. Yang W., Bielawski J.P., and Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57 2 (2003) 212-221