Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Journal of General Virology

Volumn 92, Issue 4, 2011, Pages 752-767

  Varsani, Arvind ^a,b   Regnard, Guy L ^b   Bragg, Robert ^c   Hitzeroth, Inga I ^b   Rybicki, Edward P ^b  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

^c UNIVERSITY OF THE FREE STATE   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BEAK AND FEATHER DISEASE; CIRCOVIRUS; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PSITTACINE; SPECIES DISTRIBUTION; VIRUS GENOME; VIRUS ISOLATION; VIRUS RECOMBINATION; VIRUS STRAIN;

ANIMALS; BIRD DISEASES; CIRCOVIRIDAE INFECTIONS; CIRCOVIRUS; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; PSITTACIFORMES; SEQUENCE ANALYSIS, DNA;

AVES; BEAK AND FEATHER DISEASE VIRUS; BOVINE CORONAVIRUS; CIRCOVIRUS; MELOPSITTACUS; PSITTACIFORMES;

EID: 79955751258     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.028126-0     Document Type: Article

References (60)

1. Abascal, F., Zardoya, R. & Posada, D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105.
2. Albertyn, J., Tajbhai, K. M. & Bragg, R. R. (2004). Psittacine beak and feather disease virus in budgerigars and ring-neck parakeets in South Africa. Onderstepoort J Vet Res 71, 29-34.
3. Bassami, M. R., Berryman, D., Wilcox, G. E. & Raidal, S. R. (1998). Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus. Virology 249, 453-459.
4. Bassami, M. R., Ypelaar, I., Berryman, D., Wilcox, G. E. & Raidal, S. R. (2001). Genetic diversity of beak and feather disease virus detected in psittacine species in Australia. Virology 279, 392-400.
5. Bendheim, U., Karnieli, A., Perl, S., Lublin, A. & Davidson, I. (2006). Prevalence of psittacine circovirus in Israel. Isr J Vet Med 61, 12-15.
6. Bert, E., Tomassone, L., Peccati, C., Navarrete, M. G. & Sola, S. C. (2005). Detection of beak and feather disease virus (BFDV) and avian polyomavirus (APV) DNA in psittacine birds in Italy. J Vet Med B Infect Dis Vet Public Health 52, 64-68.
7. Boni, M. F., Posada, D. & Feldman, M. W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176, 1035-1047.
8. Crowther, R. A., Berriman, J. A., Curran, W. L., Allan, G. M. & Todd, D. (2003). Comparison of the structures of three circoviruses: chicken anemia virus, porcine circovirus type 2, and beak and feather disease virus. J Virol 77, 13036-13041.
9. de Kloet, E. & de Kloet, S. R. (2004). Analysis of the beak and feather disease viral genome indicates the existence of several genotypes which have a complex psittacine host specificity. Arch Virol 149, 2393-2412.
10. Doneley, R. J. (2003). Acute beak and feather disease in juvenile African grey parrots - an uncommon presentation of a common disease. Aust Vet J 81, 206-207.
11. Duffy, S. & Holmes, E. C. (2009). Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 90, 1539-1547.
12. Fauquet, C. M., Briddon, R. W., Brown, J. K., Moriones, E., Stanley, J., Zerbini, M. & Zhou, X. (2008). Geminivirus strain demarcation and nomenclature. Arch Virol 153, 783-821.
13. Gibbs, M. J., Armstrong, J. S. & Gibbs, A. J. (2000). Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573-582.
14. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
15. Ha, H. J., Anderson, I. L., Alley, M. R., Springett, B. P. & Gartrell, B. D. (2007). The prevalence of beak and feather disease virus infection in wild populations of parrots and cockatoos in New Zealand. N Z Vet J 55, 235-238.
16. Harkins, G. W., Delport, W., Duffy, S., Wood, N., Monjane, A. L., Owor, B. E., Donaldson, L., Saumtally, S., Triton, G. & other authors (2009). Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol J 6, 104.
17. Heath, L., Martin, D. P., Warburton, L., Perrin, M., Horsfield, W., Kingsley, C., Rybicki, E. P. & Williamson, A. L. (2004). Evidence of unique genotypes of Beak and feather disease virus in Southern Africa. J Virol 78, 9277-9284.
18. Heath, L., Williamson, A. L. & Rybicki, E. P. (2006). The capsid protein of beak and feather disease virus binds to the viral DNA and is responsible for transporting the replication-associated protein into the nucleus. J Virol 80, 7219-7225.
19. Hughes, A. L. & Piontkivska, H. (2008). Nucleotide sequence polymorphism in circoviruses. Infect Genet Evol 8, 130-138.
20. Khalesi, B., Bonne, N., Stewart, M., Sharp, M. & Raidal, S. (2005). A comparison of haemagglutination, haemagglutination inhibition and PCR for the detection of psittacine beak and feather disease virus infection and a comparison of isolates obtained from loriids. J Gen Virol 86, 3039-3046.
21. Kiatipattanasakul-Banlunara, W., Tantileartcharoen, R., Katayama, K., Suzuki, K., Lekdumrogsak, T., Nakayama, H. & Doi, K. (2002). Psittacine beak and feather disease in three captive sulphur-crested cockatoos (Cacatua galerita) in Thailand. J VetMed Sci 64, 527-529.
22. Kosakovsky Pond, S. L. & Frost, S. D. (2005). Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22, 1208-1222.
23. Lefeuvre, P., Martin, D. P., Hoareau, M., Naze, F., Delatte, H., Thierry, M., Varsani, A., Becker, N., Reynaud, B. & Lett, J. M. (2007). Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination. J Gen Virol 88, 3458-3468.
24. Lefeuvre, P., Lett, J. M., Varsani, A. & Martin, D. P. (2009). Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83, 2697-2707.
25. Li, L., Kapoor, A., Slikas, B., Bamidele, O. S., Wang, C., Shaukat, S., Masroor, M. A., Wilson, M. L., Ndjango, J.-B. N. & other authors (2010). Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84, 1674-1682.
26. Martin, D. & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562-563.
27. Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C. (2005a). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98-102.
28. Martin, D. P., Williamson, C. & Posada, D. (2005b). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260-262.
29. Meehan, B. M., Creelan, J. L., McNulty, M. S. & Todd, D. (1997). Sequence of porcine circovirus DNA: affinities with plant circoviruses. J Gen Virol 78, 221-227.
30. Niagro, F. D., Forsthoefel, A. N., Lawther, R. P., Kamalanathan, L., Ritchie, B. W., Latimer, K. S. & Lukert, P. D. (1998). Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses. Arch Virol 143, 1723-1744.
31. Ogawa, H., Katoh, H., Sanada, N., Sanada, Y., Ohya, K., Yamaguchi, T. & Fukushi, H. (2010). A novel genotype of beak and feather disease virus in budgerigars (Melopsittacus undulatus). Virus Genes 2, 231-235.
32. Ortiz-Catedral, L., Kurenbach, B., Massaro, M., McInnes, K., Brunton, D. H., Hauber, M. E., Martin, D. P. & Varsani, A. (2010). A new isolate of beak and feather disease virus from endemic wild redfronted parakeets (Cyanoramphus novaezelandiae) in New Zealand. Arch Virol 155, 613-620.
33. Padidam, M., Sawyer, S. & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218-225.
34. Pass, D. A. & Perry, R. A. (1984). The pathology of psittacine beak and feather disease. Aust Vet J 61, 69-74.
35. Pond, S. L. & Frost, S. D. (2005). Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21, 2531-2533.
36. Posada, D. (2006). ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34 (Web Server), W700-W703.
37. Posada, D. & Crandall, K. A. (2002). The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 54, 396-402.
38. Rahaus, M. & Wolff, M. H. (2003). Psittacine beak and feather disease: a first survey of the distribution of beak and feather disease virus inside the population of captive psittacine birds in Germany. J Vet Med B Infect Dis Vet Public Health 50, 368-371.
39. Raidal, S. R. & Cross, G. M. (1994a). Control by vaccination of psittacine beak and feather disease in a mixed flock of Agapornis spp. Aust Vet Pract 24, 178-180.
40. Raidal, S. R., McElnea, C. L. & Cross, G. M. (1993). Seroprevalence of psittacine beak and feather disease in wild psittacine birds in New South Wales. Aust Vet J 70, 137-139.
41. Raue, R., Johne, R., Crosta, L., Bürkle, M., Gerlach, H. & Müller, H. (2004). Nucleotide sequence analysis of a C1 gene fragment of psittacine beak and feather disease virus amplified by real-time polymerase chain reaction indicates a possible existence of genotypes. Avian Pathol 33, 41-50.
42. Ritchie, B. W., Niagro, F. D., Lukert, P. D., Steffens, W. L., III & Latimer, K. S. (1989). Characterization of a new virus from cockatoos with psittacine beak and feather disease. Virology 171, 83-88.
43. Ritchie, B. W., Niagro, F. D., Latimer, K. S., Lukert, P. D., Steffens, W. L., III, Rakich, P. M. & Pritchard, N. (1990). Ultrastructural, protein composition, and antigenic comparison of psittacine beak and feather disease virus purified from four genera of psittacine birds. J Wildl Dis 26, 196-203.
44. Ritchie, P. A., Anderson, I. L. & Lambert, D. M. (2003). Evidence for specificity of psittacine beak and feather disease viruses among avian hosts. Virology 306, 109-115.
45. Sanada, Y., Sanada, N. & Kubo, M. (1999). Electron microscopical observations of psittacine beak and feather disease in an umbrella cockatoo (Cacatua alba). J Vet Med Sci 61, 1063-1065.
46. Schoemaker, N. J., Dorrestein, G. M., Latimer, K. S., Lumeij, J. T., Kik, M. J., van der Hage, M. H. & Campagnoli, R. P. (2000). Severe leukopenia and liver necrosis in young African grey parrots (Psittacus erithacus erithacus) infected with psittacine circovirus. Avian Dis 44, 470-478.
47. Shearer, P. L., Bonne, N., Clark, P., Sharp, M. & Raidal, S. R. (2008). Beak and feather disease virus infection in cockatiels (Nymphicus hollandicus). Avian Pathol 37, 75-81.
48. Shepherd, D. N., Martin, D. P., Lefeuvre, P., Monjane, A. L., Owor, B. E., Rybicki, E. P. & Varsani, A. (2008). A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods 149, 97-102.
49. Smith, J. M. (1992). Analyzing the mosaic structure of genes. J Mol Evol 34, 126-129.
50. Stanley, J., Bisaro, D. M., Briddon, R. W., Brown, J. K., Fauquet, C. M., Harrison, B. D., Rybicki, E. P. & Stenger, D. C. (2005). Geminiviridae. In Virus Taxonomy (VIIIth Report of the ICTV), pp. 301-306. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. London: Elsevier/Academic Press.
51. Studdert, M. J. (1993). Circoviridae: new viruses of pigs, parrots and chickens. Aust Vet J 70, 121-122.
52. 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.
53. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). 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, 4673-4680.
54. van der Walt, E., Martin, D. P., Varsani, A., Polston, J. E. & Rybicki, E. P. (2008). Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virol J 5, 104.
55. Varsani, A., Shepherd, D. N., Monjane, A. L., Owor, B. E., Erdmann, J. B., Rybicki, E. P., Peterschmitt, M., Briddon, R. W., Markham, P. G. & other authors (2008). Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol 89, 2063-2074.
56. Varsani, A., Monjane, A. L., Donaldson, L., Oluwafemi, S., Zinga, I., Komba, E. K., Plakoutene, D., Mandakombo, N., Mboukoulida, J. & other authors (2009). Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography. Virol J 6, 194.
57. Varsani, A., de Villiers, G. K., Regnard, G. L., Bragg, R. R., Kondiah, K., Hitzeroth, I. I. & Rybicki, E. P. (2010). A unique isolate of beak and feather disease virus isolated from budgerigars (Melopsittacus undulatus) in South Africa. Arch Virol 155, 435-439.
58. Vega-Rocha, S., Gronenborn, B., Gronenborn, A. M. & Campos-Olivas, R. (2007). Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 46, 6201-6212.
59. Wirminghaus, J. D., Downs, C. T., Symes, C. T. & Perrin, M. R. (1999). Conservation of the Cape parrot in southern Africa. S Afr J Wildl Res 29, 118-129.
60. Ypelaar, I., Bassami, M. R., Wilcox, G. E. & Raidal, S. R. (1999). A universal polymerase chain reaction for the detection of psittacine beak and feather disease virus. Vet Microbiol 68, 141-148.