Genetic diversity of avian paramyxovirus type 1: Proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes

Infection, Genetics and Evolution

Volumn 12, Issue 8, 2012, Pages 1770-1779

  Diel, Diego G ^a   da Silva, Luciana H A ^a,b   Liu, Hualei ^c   Wang, Zhiliang ^c   Miller, Patti J ^a   Afonso, Claudio L ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c National Reference Laboratory for Newcastle Disease   (China)

Author keywords

APMV 1; Epidemiology; Evolution; Genotyping; NDV; Newcastle disease

Indexed keywords

ARTICLE; GENE SEQUENCE; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; NEWCASTLE DISEASE PARAMYXOVIRUS; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; VIRUS CLASSIFICATION; VIRUS GENE;

ANIMALS; BIRDS; EVOLUTION, MOLECULAR; GENES, VIRAL; GENETIC VARIATION; GENOTYPE; NEWCASTLE DISEASE; NEWCASTLE DISEASE VIRUS; PHYLOGENY; RECOMBINATION, GENETIC;

APPLE MOSAIC VIRUS; NEWCASTLE DISEASE VIRUS;

EID: 84865849138     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2012.07.012     Document Type: Article

References (58)

1. Afonso C.L. Not so fast on recombination analysis of Newcastle disease virus. J. Virol. 2008, 82(18):9303.
2. Aldous E.W., Mynn J.K., Banks J., Alexander D.J. 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. 2003, 32(3):239-256.
3. Alexander D.J., Senne D.A. Newcastle disease, other avian paramyxoviruses, and pneumovirus infections. Diseases of Poultry 2008, 750-798. Blackwell Publishing, Ames, IA. 12th ed. Y.M. Saif, A.M. Fadly, J.R. Glisson, L.R. McDougald, L.K. Nolan, D. Swayne (Eds.).
4. Alexander D.J. Newcastle disease in the European Union 2000 to 2009. Avian Pathol. 2011, 40(6):547-558.
5. Cattoli G., Fusaro A., Monne I., Molia S., Le Menach A., Maregeya B., Nchare A., Bangana I., Maina A.G., Koffi J.N., Thiam H., Bezeid O.E., Salviato A., Nisi R., Terregino C., Capua I. Emergence of a new genetic lineage of Newcastle disease virus in West and Central Africa implications for diagnosis and control. Vet. Microbiol. 2010, 142(3-4):168-176.
6. Chare E.R., Gould E.A., Holmes E.C. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 2003, 84:2691-2703.
7. Collins P., Bukreyev A., Murphy B.R. What are the risks-hypothetical and observed of recombination involving live vaccines and vaccine vectors based on nonsegmented negative-strain RNA viruses?. J. Virol. 2008, 82(19):9805-9806.
8. Czeglédi A., Ujvári D., Somogyi E., Wehmann E., Werner O., Lomniczi B. Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications. Virus Res. 2006, 120(1-2):36-48.
9. de Leeuw O.S., Hartog L., Koch G., Peeters B.P.H. Effect of fusion protein cleavage site mutations on virulence of Newcastle disease virus: non-virulent cleavage site mutants revert to virulence after one passage in chicken brain. J. Gen. Virol. 2003, 84(2):475-484.
10. de Leeuw O.S., Koch G., Hartog L., Ravenshorst N., Peeters B.P.H. Virulence of Newcastle disease virus is determined by the cleavage site of the fusion protein and by both the stem region and globular head of the haemagglutinin-neuraminidase protein. J. Gen. Virol. 2005, 86(6):1759-1769.
11. de Vienne D.M., Giraud T., Martin O.C. A congruence index for testing topological simirarity between trees. Bioinformat. 2007, 23(23):3119-3124.
12. Diel D.G., Susta L., Cardenas Garcia S., Killian M.L., Brown C.C., Miller P.J., Afonso C.L. Complete genome and clinicopathological characterization of a virulent newcastle disease virus isolate from South America. J. Clin. Microbiol. 2012, 50(2):378-387.
13. Diel D.G., Miller P.J., Wolf P.C., Mickley R.M., Musante A.R., Emanuali D.C., Shively K.J., Pedersen K., Afonso C.L. Characterization of newcastle disease viruses isolated from cormorant and gull species in the United States in 2010. Avian Dis. 2011, 56:128-133.
14. Guindon S., Gascuel O. A simplest, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52(5):696-704.
15. Han G.-Z., He C.Q., Ding N.Z., Ma L.Y. Identification of a natural multi-recombinant of Newcastle disease virus. Virol. 2008, 371:54-60.
16. Han G.-Z., Worobey M. Homologous recombination in negative sense RNA viruses. Viruses 2011, 3:1358-1373.
17. Holland J., Spindler K., Horodyski F., Grabau E., Nichol S., Vande P.S. Rapid evolution of RNA genomes. Science 1982, 215:1577-1585.
18. Hu S., Ma H., Wu Y., Liu W., Wang X., Liu Y., Liu X. A vaccine candidate of attenuated genotype VII Newcastle disease virus generated by reverse genetics. Vaccine 2009, 27(6):904-910.
19. Hu Z., Hu S., Meng C., Wang X., Zhu J., Liu X. Generation of a genotype VII Newcastle disease virus vaccine candidate with high yield in embryonated chicken eggs. Avian Dis. 2011, 55(3):391-397.
20. Huang Y., Wan H.Q., Liu H.Q., Wu Y.T., Liu X.F. Genomic sequence of an isolate of Newcastle disease virus isolated from an outbreak in geese: a novel six nucleotide insertion in the non-coding region of the nucleoprotein gene. Brief Report. Arch. Virol. 2004, 149(7):1445-1457.
21. IASA - Investigación Aplicada S.A. de C.V., 2012. Genovax N5. Retrieved from http://www.engormix.com/iasa-investigacion-aplicada/genovax-sh10043_pr26921.htm.
22. Khan T.A., Rue C.A., Rehmani S.F., Ahmed A., Wasilenko J.L., Miller P.J., Afonso C.L. Phylogenetic and biological characterization of Newcastle disease virus isolates from Pakistan. J. Clin. Microbiol. 2010, 48(5):1892-1894.
23. 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., Afonso C.L. Phylogenetic diversity among low-virulence Newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates. J. Virol. 2007, 81(22):12641-12653.
24. Kim L.M., King D.J., Guzman H., Tesh R.B., Travassos da Rosa A.P.A., Bueno R., Dennett J.A., Afonso C.L. Biological and phylogenetic characterization of pigeon paramyxovirus serotype 1 circulating in wild North American pigeons and doves. J. Clin. Microbiol. 2008, 46(10):3303-3310.
25. Kim L.M., King D.J., Suarez D.L., Wong C.W., Afonso C.L. 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. 2007, 45(4):1310-1314.
26. Kinde H., Hullinger P.J., Charlton B., McFarland M., Hietala S.K., Velez V., Case J.T., Garber L., Wainwright S.H., Mikolon A.B., Breitmeyer R.E., Ardans A.A. The isolation of exotic Newcastle disease (END) virus from nonpoultry avian species associated with the epidemic of END in chickens in southern California: 2002-2003. Avian Dis. 2005, 49(2):195-198.
27. Kommers G.D., King D.J., Seal B.S., Brown C.C. Virulence of pigeon-origin Newcastle disease virus isolates for domestic chickens. Avian Dis. 2001, 45(4):906-921.
28. Kommers G.D., King D.J., Seal B.S., Carmichael K.P., Brown C.C. Pathogenesis of six pigeon-origin isolates of Newcastle disease virus for domestic chickens. Vet. Pathol. 2002, 39(3):353-362.
29. Liu X.F., Wan H.Q., Ni X.X., Wu Y.T., Liu W.B. 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. 2003, 148(7):1387-1403.
30. Maminiaina O.F., Gil P., Briand F.-X., Albina E., Keita D., Andriamanivo H.R., Chevalier V., Lancelot R., Martinez D., Rakotondravao R., Rajaonarison J.J., Koko M., Andriantsimahavandy A.A., Jestin V., Servan de Almeida R. Newcastle disease virus in Madagascar: identification of an original genotype possibly deriving from a died out ancestor of genotype IV. PloS One 2010, 5(11):e13987.
31. Martin D.P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinfomat 2010, 26:2462-2463.
32. Miller P.J., Decanini E.L., Afonso C.L. Newcastle disease: Evolution of genotypes and the related diagnostic challenges. Infect. Gen. Evol. 2010, 10(1):26-35.
33. Miller P.J., Estevez C., Yu Q., Suarez D.L., King D.J. Comparison of viral shedding following vaccination with inactivated and live Newcastle disease vaccines formulated with wild-type and recombinant viruses. Avian Dis. 2009, 53(1):39-49.
34. Miller P.J., Kim L.M., Ip H.S., Afonso C.L. Evolutionary dynamics of Newcastle disease virus. Virol. 2009, 391(1):64-72.
35. Miller P.J., King D.J., Afonso C.L., Suarez D.L. Antigenic differences among Newcastle disease virus strains of different genotypes used in vaccine formulation affect viral shedding after a virulent challenge. Vaccine. 2007, 25(41):7238-7246.
36. Nei M., Kumar S. Molecular Evolution and Phylogenetics 2000, University Press, New York, NY, p. 333.
37. Pedersen J.C., Senne D.A., Woolcock P.R., Kinde H., King D.J., Wise M.G., Panigrahy B., Seal B.S. Phylogenetic relationships among virulent Newcastle disease virus isolates from the 2002-2003 outbreak in California and other recent outbreaks in North America. J. Clin. Microbiol. 2004, 42(5):2329-2334.
38. Perozo F., Merino R., Afonso C.L., Villegas P., Calderon N. Biological and phylogenetic characterization of virulent Newcastle disease virus circulating in Mexico. Avian Dis. 2008, 52(3):472-479.
39. Perozo F., Marcano R., Afonso C.L. Biological and Phylogenetic Characterization of a Genotype VII Newcastle Disease Virus from Venezuela: Efficacy of field Vaccination. J. Clin. Microbiol. 2012, 10.1128/JCM.06,506-11.
40. Qin Z., Sun L., Ma B., Cui Z., Zhu Y., Kitamura Y., Liu W. F gene recombination between genotype II and VII Newcastle disease virus. Virus Res. 2008, 131:299-303.
41. Qin Z.-M., Tan L.-T., Xu H.-Y., Ma B.-C., Wang Y.-L., Yuan X.-Y., 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. 2008, 46(2):601-611.
42. Qiu X., Sun Q., Wu S., Dong L., Hu S., Meng C., Wu Y., Liu X. Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size. Virol. J. 2011, 8:117.
43. Rue C.A., Susta L., Brown C.C., Pasick J.M., Swafford S.R., Wolf P.C., Killian M.L., Pedersen J.C., Miller P.J., Afonso C.L. Evolutionary changes affecting rapid identification of 2008 Newcastle disease viruses isolated from double-crested cormorants. J. Clin. Microbiol. 2010, 48(7):2440-2448.
44. Seal B.S., King D.J., Bennett J.D. Characterization of Newcastle disease virus isolates by reverse transcription PCR coupled to direct nucleotide sequencing and development of sequence database for pathotype prediction and molecular epidemiological analysis. J. Clin. Microbiol. 1995, 33(10):2624-2630.
45. Snoeck C.J., Ducatez M.F., Owoade A.A., Faleke O.O., Alkali B.R., Tahita M.C., Tarnagda Z., Ouedraogo J.B., Maikano I., Mbah P.O., Kremer J.R., Muller C.P. Newcastle disease virus in West Africa: new virulent strains identified in non-commercial farms. Arch. Virol. 2009, 154(1):47-54.
46. Song Q., Cao Y., Li Q., Gu M., Zhong L., Hu S., Wan H., Liu X. Artificial recombination may influence the evolutionary analysis of Newcastle disease virus. J Virol. 2011, 85(4):10409-10414.
47. Tamura K., Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 2002, 19(10):1727-1736.
48. Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Nat. Acad. Sci. USA 2004, 101:11030-11035.
49. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. Mega5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28(10):2731-2739.
50. Tan S.W., Ideris A., Omar A.R., Yusoff K., Hair-Bejo M. Sequence and phylogenetic analysis of Newcastle disease virus genotypes isolated in Malaysia between 2004 and 2005. Arch. Virol. 2010, 155(1):63-70.
51. Tsai H.-J., Chang K.-H., Tseng C.-H., Frost K.M., Manvell R.J., Alexander D.J. Antigenic and genotypical characterization of Newcastle disease viruses isolated in Taiwan between 1969 and 1996. Vet. Microbiol. 2004, 104(1-2):19-30.
52. WHO/OIE/FDA and Evolution Working Group Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1). Em. Infect. Dis. 2008, 14(7):e1.
53. Wang Z., Liu H., Xu J., Bao J., Zheng D., Sun C., Wei R., Song C., Chen J. Genotyping of Newcastle disease viruses isolated from 2002 to 2004 in China. An. N. Y. Acad. Sci. 2006, 1081:228-239.
54. Wehmann E., Czeglédi A., Werner O., Kaleta E.F., Lomniczi B. Occurrence of genotypes IV, V, VI and VIIa in Newcastle disease outbreaks in Germany between 1939 and 1995. Avian Pathol. 2003, 32(2):157-163.
55. Wu S., Wang W., Yao C., Wang X., Hu S., Cao J., Wu Y., Liu W., Liu X. Genetic diversity of Newcastle disease viruses isolated from domestic poultry species in Eastern China during 2005-2008. Arch. Virol. 2010, Epub ahead of print. 10.1007/s00705-010-0851-5.
56. Yu L., Wang Z., Jiang Y., Chang L., Kwang J. Characterization of newly emerging Newcastle disease virus isolates from the People's Republic of China and Taiwan. J. Clin. Microbiol. 2001, 39(10):3512-3519.
57. Zhang R., Wag X., Su J., Zhao J., Zhang G. Isolation and analysis of two naturally occurring multi-recombination Newcastle disease viruses in China. Virus Res. 2010, 151:45-53.
58. Zhang S., Wang X., Zhao C., Liu D., Hu Y., Zhao J., Zhang G. Phylogenetic and Pathotypical Analysis of Two Virulent Newcastle Disease Viruses Isolated from Domestic Ducks in China. PloS One 2011, 6(9):e25000.