The effect of vaccination on the evolution and population dynamics of Avian Paramyxovirus-1

PLoS Pathogens

Volumn 6, Issue 4, 2010, Pages 1-11

  Chong, Yee Ling ^a   Padhi, Abinash ^a   Hudson, Peter J ^a,b   Poss, Mary ^a,b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN; LIVE VACCINE;

ARTICLE; AVULAVIRUS; CONTROLLED STUDY; GENETIC IDENTIFICATION; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION DYNAMICS; POPULATION SIZE; PROMOTER REGION; RECOMBINANT GENE; VACCINATION; VIRUS GENOME; VIRUS STRAIN; ANIMAL; BIRD DISEASE; EVOLUTION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NEWCASTLE DISEASE; NEWCASTLE DISEASE PARAMYXOVIRUS; POULTRY;

APPLE MOSAIC VIRUS; AVES; NEWCASTLE DISEASE VIRUS; PARAMYXOVIRIDAE;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; GENOME, VIRAL; GENOTYPE; MOLECULAR SEQUENCE DATA; NEWCASTLE DISEASE; NEWCASTLE DISEASE VIRUS; PHYLOGENY; POPULATION DYNAMICS; POULTRY; POULTRY DISEASES; VACCINATION; VACCINES, ATTENUATED;

EID: 77954056068     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1000872     Document Type: Article

References (81)

1. Kaleta EF, Baldauf C (1988) Newcastle disease in free living and pet birds. In: Alexander DJ, ed. Newcastle Disease. Boston: Kluwer Academic Publishers. Pp 197-246.
2. Spradbrow PB (1987) Newcastle Disease - An Overview. In: Copland JW, ed. Newcastle Disease in Poultry: A New Food Pellet Vaccine. Melbourne: Ramsay Ware Printing. pp 12-18.
3. Alexander DJ (1988) Newcastle Disease Virus - An Avian Paramyxovirus. In: Alexander DJ, ed. Newcastle Disease. Boston: Kluwer Academic Publishers. pp 11-22.
4. Leighton FA, Heckert RA (2007) Newcastle disease and related avian Paramyxoviruses. In: Thomas NJ, Hunter DB, Atkinson CT, eds. Infectious diseases of wild birds. Oxford: Blackwell Publishing. pp 3-16.
5. Kim LM, King DJ, Suarez DL, Wong CW, Afonso CL (2007) Characterization of class I Newcastle disease virus isolates from Hong Kong live bird markets and detection using real-time reverse transcription-PCR. J Clin Microbiol 45: 1310-1314.
6. Hitchner SB (1964) Control of Newcastle Disease in the United States by Vaccination. In: Hanson RP, ed. Newcastle Disease Virus: An Evolving Pathogen/proceedings of an international symposium. Madison: The University of Wisconsin Press. pp 85-98.
7. Kapczynski DR, King DJ (2005) Protection of chickens against overt clinical disease and determination of viral shedding following vaccination with commercially available Newcastle disease virus vaccines upon challenge with highly virulent virus from the California 2002 exotic Newcastle disease outbreak. Vaccine 23: 3424-3433.
8. Miller P, King DJ, Afonso C, Suarez D (2007) Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge. Vaccine 25: 7238-7246.
9. van Boven M, Bouma A, Fabri THF, Katsma E, Hartog L, et al. (2008) Herd immunity to Newcastle disease virus in poultry by vaccination. Avian Pathol 37: 1-5.
10. de Leeuw O, Peeters B (1999) Complete nucleotide sequence of Newcastle disease virus: evidence for the existence of a new genus within the subfamily Paramyxovirinae. J Gen Virol 80: 131-136.
11. Mayo MA (2002) Virus taxonomy - Houston 2002. Arch Virol 147: 1071-1076.
12. Steward M, Vipond IB, Millar NS, Emmerson PT (1993) RNA editing in Newcastle disease virus. J Gen Virol 74(Pt 12): 2539-2547.
13. Czegledi A, Ujvari D, Somogyi E, Wehmann E, Werner O, et al. (2006) Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications. Virus Res 120: 36-48.
14. Seal BS, Wise MG, Pedersen JC, Senne DA, Alvarez R, et al. (2005) Genomic sequences of low-virulence avian paramyxovirus-1 (Newcastle disease virus) isolates obtained from live-bird markets in North America not related to commonly utilized commercial vaccine strains. Vet Microbiol 106: 7-16.
15. Kattenbelt JA, Stevens MP, Gould AR (2006) Sequence variation in the Newcastle disease virus genome. Virus Res 116: 168-184.
16. Miller PJ, Decanini EL, Afonso CL (2010) Newcastle disease: Evolution of genotypes and the related diagnostic challenges. Infect Genet Evol 10: 26-35.
17. Wehmann E, Czegledi A, Werner O, Kaleta EF, Lomniczi B (2003) Occurrence of genotypes IV, V, VI and VIIa in Newcastle disease outbreaks in Germany between 1939 and 1995. Avian Pathol 32: 157-163.
18. Kwon HJ, Cho SH, Ahn YJ, Seo SH, Choi KS, et al. (2003) Molecular epidemiology of Newcastle disease in Republic of Korea. Vet Microbiol 95: 39-48.
19. Aldous EW, Mynn JK, Banks J, Alexander DJ (2003) A molecular epidemiological study of avian paramyxovirus type 1 (Newcastle disease virus) isolates by phylogenetic analysis of a partial nucleotide sequence of the fusion protein gene. Avian Pathol 32: 239-257.
20. Huang Z, Elankumaran S, Yunus AS, Samal SK (2004) A recombinant Newcastle disease virus (NDV) expressing VP2 protein of infectious bursal disease virus (IBDV) protects against NDV and IBDV. J Virol 78: 10054-10063.
21. Lee YJ, Sung HW, Choi JG, Kim JH, Song CS (2004) Molecular epidemiology of Newcastle disease viruses isolated in South Korea using sequencing of the fusion protein cleavage site region and phylogenetic relationships. Avian Pathol 33: 482-491.
22. Liu XF, Wan HQ, Ni XX, Wu YT, Liu WB (2003) Pathotypical and genotypical characterization of strains of Newcastle disease virus isolated from outbreaks in chicken and goose flocks in some regions of China during 1985-2001. Arch Virol 148: 1387-1403.
23. Mase M, Imai K, Sanada Y, Sanada N, Yuasa N, et al. (2002) Phylogenetic analysis of Newcastle disease virus genotypes isolated in Japan. J Clin Microbiol 40: 3826-3830.
24. Tsai HJ, Chang KH, Tseng CH, Frost KM, Manvell RJ, et al. (2004) Antigenic and genotypical characterization of Newcastle disease viruses isolated in Taiwan between 1969 and 1996. Vet Microbiol 104: 19-30.
25. Moya A, Elena SF, Bracho A, Miralles R, Barrio E (2000) The evolution of RNA viruses: A population genetics view. Proc Natl Acad Sci U S A 97: 6967-6973.
26. Elena SF, Sanjuan R (2005) Adaptive value of high mutation rates of RNA viruses: separating causes from consequences. J Virol 79: 11555-11558.
27. Bruen TC, Poss M (2007) Recombination in feline immunodeficiency virus genomes from naturally infected cougars. Virology 364: 362-370.
28. Herrewegh AA, Smeenk I, Horzinek MC, Rottier PJ, de Groot RJ (1998) Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J Virol 72: 4508-4514.
29. Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, et al. (2009) Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324: 55-59.
30. Sakaguchi T, Toyoda T, Gotoh B, Inocencio NM, Kuma K, et al. (1989) Newcastle disease virus evolution. I. Multiple lineages defined by sequence variability of the hemagglutinin-neuraminidase gene. Virology 169: 260-272.
31. Toyoda T, Sakaguchi T, Hirota H, Gotoh B, Kuma K, et al. (1989) Newcastle disease virus evolution. II. Lack of gene recombination in generating virulent and avirulent strains. Virology 169: 273-282.
32. Han GZ, He CQ, Ding NZ, Ma LY (2008) Identification of a natural multirecombinant of Newcastle disease virus. Virology 371: 54-60.
33. Miller PJ, Kim LM, Ip HS, Afonso CL (2009) Evolutionary dynamics of Newcastle disease virus. Virology 391: 64-72.
34. Qin Z, Sun L, Ma B, Cui Z, Zhu Y, et al. (2008) F gene recombination between genotype II and VII Newcastle disease virus. Virus Res 131: 299-303.
35. Becher P, Orlich M, Thiel HJ (2001) RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease. J Virol 75: 6256-6264.
36. Georgescu MM, Delpeyroux F, Crainic R (1995) Tripartite genome organization of a natural type 2 vaccine/nonvaccine recombinant poliovirus. J Gen Virol 76(Pt 9): 2343-2348.
37. Guillot S, Caro V, Cuervo N, Korotkova E, Combiescu M, et al. (2000) Natural genetic exchanges between vaccine and wild poliovirus strains in humans. J Virol 74: 8434-8443.
38. Hon CC, Lam TT, Yip CW, Wong RT, Shi M, et al. (2008) Phylogenetic evidence for homologous recombination within the family Birnaviridae. J Gen Virol 89: 3156-3164.
39. Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
40. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21: 260-262.
41. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
42. 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.
43. Seal BS (1996) Analysis of Matrix Protein Gene Nucleotide Sequence Diversity Among Newcastle Disease Virus Isolates Demonstrates that Recent Disease Outbreaks Are Caused by Viruses of Psittacine Origin. Virus Genes 11: 217-224.
44. Maddison WP (1997) Gene Trees in Species Trees. Syst Biol 46: 523-536.
45. Seal BS, King DJ, Meinersmann RJ (2000) Molecular evolution of the Newcastle disease virus matrix protein gene and phylogenetic relationships among the paramyxoviridae. Virus Res 66: 1-11.
46. Lai MM (1992) RNA recombination in animal and plant viruses. Microbiol Mol Biol Rev 56: 61-79.
47. Chare ER, Gould EA, Holmes EC (2003) Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J Gen Virol 84: 2691-2703.
48. Geue L, Schares S, Schnick C, Kliemt J, Beckert A, et al. (2008) Genetic characterisation of attenuated SAD rabies virus strains used for oral vaccination of wildlife Vaccine 26: 3227-3235.
49. McCarthy AJ, Shaw MA, Goodman SJ (2007) Pathogen evolution and disease emergence in carnivores. Proc Biol Sci 274: 3165-3174.
50. Wittmann TJ, Biek R, Hassanin A, Rouquet P, Reed P, et al. (2007) Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants. Proc Natl Acad Sci U S A 104: 17123-17127.
51. Afonso CL (2008) Not so fast on recombination analysis of Newcastle disease virus. J Virol 82: 9303.
52. Okoye JO, Shoyinka SV (1983) Newcastle disease in a vaccinated flock which had experienced subclinical infectious bursal disease. Trop Anim Health Prod 15: 221-225.
53. Cho SH, Kim SJ, Kwon HJ (2007) Genomic sequence of an antigenic variant Newcastle disease virus isolated in Korea. Virus Genes 35: 293-302.
54. Chen JP, Wang CH (2002) Phylogenetic analysis of Newcastle disease virus in Taiwan. J Microbiol Immunol Infect 35: 223-228.
55. Tan LT, Xu HY, Wang YL, Qin ZM, Sun L, et al. (2008) Molecular characterization of three new virulent Newcastle disease virus variants isolated in China. J Clin Microbiol 46: 750-753.
56. Padhi A, Poss M (2009) Population dynamics and rates of molecular evolution of a recently emerged paramyxovirus, avian metapneumovirus subtype C. J Virol 83: 2015-2019.
57. Pomeroy LW, Bjornstad ON, Holmes EC (2008) The evolutionary and epidemiological dynamics of the paramyxoviridae. J Mol Evol 66: 98-106.
58. 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.
59. Macpherson LW (1956) Some observations on the epizootiology of New Castle Disease. Can J Comp Med Vet Sci 20: 155-168.
60. Kovats RS, Bouma MJ, Haines A (1999) World Health Organization - Sustainable Development and Healthy Environments: El Niño and Health. Geneva.
61. Bridges CB, Lim W, Hu-Primmer J, Sims L, Fukuda K, et al. (2002) Risk of influenza A (H5N1) infection among poultry workers, Hong Kong, 1997-1998. J Infect Dis 185: 1005-1010.
62. Chan PK (2002) Outbreak of avian influenza A(H5N1) virus infection in Hong Kong in 1997. Clin Infect Dis 34 Suppl 2: S58-64.
63. Holmes EC (2009) The Evolution and Emergence of RNA Viruses. Great Britain: Oxford University Press. 254 p.
64. Gould AR, Kattenbelt JA, Selleck P, Hansson E, Della-Porta A, et al. (2001) Virulent Newcastle disease in Australia: molecular epidemiological analysis of viruses isolated prior to and during the outbreaks of 1998-2000. Virus Res 77: 51-60.
65. Peeters BP, deLeeuw OS, Koch G, Gielkens AL (1999) Rescue of Newcastle disease virus from cloned cDNA: evidence that cleavability of the fusion protein is a major determinant for virulence. J Virol 73: 5001-5009.
66. Westbury H (2001) Newcastle disease virus: an evolving pathogen? Avian Pathol 30: 5-11.
67. Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test to detect adaptive molecular evolution. Mol Biol Evol 18: 1585-1592.
68. 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.
69. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
70. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sunderland, Massachusetts: Sinauer Associates.
71. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
72. Shimodaira H, Hasegawa M (1999) Letter to the Editor Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference. Mol Biol Evol 16: 1114-1116.
73. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225.
74. Smith JM (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
75. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98: 13757-13762.
76. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
77. Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047.
78. Heled J, Drummond AJ (2008) Bayesian inference of population size history from multiple loci. BMC Evol Biol 8: 289.
79. Anisimova M, Nielsen R, Yang Z (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236.
80. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 13: 555-556.
81. Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.