Screening of feral and wood pigeons for viruses harbouring a conserved mobile viral element: Characterization of novel astroviruses and picornaviruses

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Kofstad, Tone ^a   Jonassen, Christine M ^a,b  

^a NORWEGIAN VETERINARY INSTITUTE   (Norway)

^b AKERSHUS UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; ASTROVIRUS; CONTROLLED STUDY; GENE DOSAGE; NEW SPECIES; NONHUMAN; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; PICORNAVIRUS; PICORNAVIRUS A; PICORNAVIRUS B; PIGEON; RNA ANALYSIS; RNA STRUCTURE; SCREENING TEST; STEM LOOP 2M LIKE MOTIF; UNINDEXED SEQUENCE; VIRUS CHARACTERIZATION; VIRUS DETECTION; VIRUS IDENTIFICATION; ANIMAL; CHEMISTRY; CONFORMATION; GENETICS; PIGEONS AND DOVES; VIROLOGY; VIRUS;

ASTROVIRIDAE; AVASTROVIRUS; AVES; CALICIVIRIDAE; COLUMBA; CORONAVIRIDAE; MAMMALIA; PICORNAVIRIDAE; RNA VIRUSES;

ANIMALS; AVASTROVIRUS; COLUMBIDAE; CONSERVED SEQUENCE; NUCLEIC ACID CONFORMATION; PICORNAVIRIDAE; RNA, VIRAL; VIRUSES;

EID: 80054735130     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025964     Document Type: Article

References (59)

1. Jonassen CM, Jonassen TO, Grinde B, (1998) A common RNA motif in the 3′ end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J Gen Virol 79 (Pt 4): 715-718.
2. Finkbeiner SR, Kirkwood CD, Wang D, (2008) Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. Virol J 5: 117.
3. Rivera R, Nollens HH, Venn-Watson S, Gulland FM, Wellehan JF Jr, (2010) Characterization of phylogenetically diverse astroviruses of marine mammals. J Gen Virol 91: 166-173.
4. Koci MD, Seal BS, Schultz-Cherry S, (2000) Molecular Characterization of an Avian Astrovirus. J Virol 74: 6173-6177.
5. Chu DK, Chin AW, Smith GJ, Chan KH, Guan Y, et al. (2010) Detection of novel astroviruses in urban brown rats and previously known astroviruses in human. J Gen Virol 91 (Pt 10): 2457-2462.
6. Zhu HC, Chu DK, Liu W, Dong BQ, Zhang SY, et al. (2009) Detection of diverse astroviruses from bats in China. J Gen Virol 90 (Pt 4): 883-887.
7. Wutz G, Auer H, Nowotny N, Grosse B, Skern T, et al. (1996) Equine rhinovirus serotypes 1 and 2: relationship to each other and to aphthoviruses and cardioviruses. J Gen Virol 77 (Pt 8): 1719-1730.
8. Woo PC, Lau SK, Huang Y, Lam CS, Poon RW, et al. (2010) Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae. J Gen Virol 91: 2433-2448.
9. Jonassen CM, Kofstad T, Larsen IL, Lovland A, Handeland K, et al. (2005) Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos). J Gen Virol 86: 1597-1607.
10. Woo PC, Lau SK, Huang Y, Yuen KY, (2009) Coronavirus diversity, phylogeny and interspecies jumping. Exp Biol Med (Maywood) 234: 1117-1127.
11. Martella V, Decaro N, Lorusso E, Radogna A, Moschidou P, et al. (2009) Genetic heterogeneity and recombination in canine noroviruses. J Virol 83: 11391-11396.
12. Mesquita JR, Barclay L, Nascimento MS, Vinje J, (2010) Novel norovirus in dogs with diarrhea. Emerg Infect Dis 16: 980-982.
13. Martella V, Lorusso E, Decaro N, Elia G, Radogna A, et al. (2008) Detection and molecular characterization of a canine norovirus. Emerg Infect Dis 14: 1306-1308.
14. Thiel HJ, Konig M, (1999) Caliciviruses: an overview. Vet Microbiol 69: 55-62.
15. Clarke IN, Lambden PR, (2000) Organization and expression of calicivirus genes. J Infect Dis 181 (Suppl 2): S309-S316.
16. Monceyron C, Grinde B, Jonassen TO, (1997) Molecular characterisation of the 3′-end of the astrovirus genome. Arch Virol 142: 699-706.
17. Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, et al. (2005) The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 3: e5.
18. Lai MM, (1992) RNA recombination in animal and plant viruses. Microbiol Rev 56: 61-79.
19. Simmonds P, (2006) Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses. J Virol 80: 11124-11140.
20. Simmonds P, Welch J, (2006) Frequency and dynamics of recombination within different species of human enteroviruses. J Virol 80: 483-493.
21. Tapparel C, Junier T, Gerlach D, Van-Belle S, Turin L, et al. (2009) New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerg Infect Dis 15: 719-726.
22. Pantin-Jackwood MJ, Spackman E, Woolcock PR, (2006) Phylogenetic analysis of Turkey astroviruses reveals evidence of recombination. Virus Genes 32: 187-192.
23. Walter JE, Briggs J, Guerrero ML, Matson DO, Pickering LK, et al. (2001) Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children. Arch Virol 146: 2357-2367.
24. Strain E, Kelley LA, Schultz-Cherry S, Muse SV, Koci MD, (2008) Genomic analysis of closely related astroviruses. J Virol 82: 5099-5103.
25. Koonin EV, Dolja VV, (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28: 375-430.
26. Worobey M, Holmes EC, (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80 (Pt 10): 2535-2543.
27. Lillehaug A, Monceyron JC, Bergsjo B, Hofshagen M, Tharaldsen J, et al. (2005) Screening of feral pigeon (Colomba livia), mallard (Anas platyrhynchos) and graylag goose (Anser anser) populations for Campylobacter spp., Salmonella spp., avian influenza virus and avian paramyxovirus. Acta Vet Scand 46: 193-202.
28. Jonassen CM, (2008) Detection and sequence characterization of the 3′-end of coronavirus genomes harboring the highly conserved RNA motif s2m. Methods Mol Biol 454: 27-34.
29. Jonassen CM, Jonassen TT, Sveen TM, Grinde B, (2003) Complete genomic sequences of astroviruses from sheep and turkey: comparison with related viruses. Virus Res 91: 195-201.
30. Tang Y, Ismail MM, Saif YM, (2005) Development of antigen-capture enzyme-linked immunosorbent assay and RT-PCR for detection of turkey astroviruses. Avian Dis 49: 182-188.
31. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
32. Kaku Y, Sarai A, Murakami Y, (2001) Genetic reclassification of porcine enteroviruses. J Gen Virol 82: 417-424.
33. Tseng CH, Tsai HJ, (2007) Sequence analysis of a duck picornavirus isolate indicates that it together with porcine enterovirus type 8 and simian picornavirus type 2 should be assigned to a new picornavirus genus. Virus Res 129: 104-114.
34. Oberste MS, Maher K, Pallansch MA, (2003) Genomic evidence that simian virus 2 and six other simian picornaviruses represent a new genus in Picornaviridae. Virology 314: 283-293.
35. Kamer G, Argos P, (1984) Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12: 7269-7282.
36. Krumbholz A, Dauber M, Henke A, Birch-Hirschfeld E, Knowles NJ, et al. (2002) Sequencing of porcine enterovirus groups II and III reveals unique features of both virus groups. J Virol 76: 5813-5821.
37. Hellen CU, de Breyne S, (2007) A distinct group of hepacivirus/pestivirus-like internal ribosomal entry sites in members of diverse picornavirus genera: evidence for modular exchange of functional noncoding RNA elements by recombination. J Virol 81: 5850-5863.
38. Fernandez-Miragall O, Lopez de QS, Martinez-Salas E, (2009) Relevance of RNA structure for the activity of picornavirus IRES elements. Virus Res 139: 172-182.
39. Kapoor A, Victoria J, Simmonds P, Wang C, Shafer RW, et al. (2008) A highly divergent picornavirus in a marine mammal. J Virol 82: 311-320.
40. Koci MD, Schultz-Cherry S, (2002) Avian astroviruses. Avian Pathol 31: 213-227.
41. Chu DK, Poon LL, Guan Y, Peiris JS, (2008) Novel astroviruses in insectivorous bats. J Virol 82: 9107-9114.
42. Mittelholzer C, Hedlund KO, Englund L, Dietz HH, Svensson L, (2003) Molecular characterization of a novel astrovirus associated with disease in mink. J Gen Virol 84: 3087-3094.
43. Fu Y, Pan M, Wang X, Xu Y, Xie X, et al. (2009) Complete sequence of a duck astrovirus associated with fatal hepatitis in ducklings. J Gen Virol 90: 1104-1108.
44. Jonassen CM, Jonassen TO, Saif YM, Snodgrass DR, Ushijima H, et al. (2001) Comparison of capsid sequences from human and animal astroviruses. J Gen Virol 82: 1061-1067.
45. Krishna NK, (2005) Identification of structural domains involved in astrovirus capsid biology. Viral Immunol 18: 17-26.
46. Wang QH, Kakizawa J, Wen LY, Shimizu M, Nishio O, et al. (2001) Genetic analysis of the capsid region of astroviruses. J Med Virol 64: 245-255.
47. Belsham GJ, (2009) Divergent picornavirus IRES elements. Virus Res 139: 183-192.
48. Chard LS, Kaku Y, Jones B, Nayak A, Belsham GJ, (2006) Functional analyses of RNA structures shared between the internal ribosome entry sites of hepatitis C virus and the picornavirus porcine teschovirus 1 Talfan. J Virol 80: 1271-1279.
49. Harris JR, Racaniello VR, (2005) Amino acid changes in proteins 2B and 3A mediate rhinovirus type 39 growth in mouse cells. J Virol 79: 5363-5373.
50. Pacheco JM, Henry TM, O'Donnell VK, Gregory JB, Mason PW, (2003) Role of nonstructural proteins 3A and 3B in host range and pathogenicity of foot-and-mouth disease virus. J Virol 77: 13017-13027.
51. Mandoki M, Bakonyi T, Ivanics E, Nemes C, Dobos-Kovacs M, et al. (2006) Phylogenetic diversity of avian nephritis virus in Hungarian chicken flocks. Avian Pathol 35: 224-229.
52. Toffan A, Jonassen CM, De BC, Schiavon E, Kofstad T, et al. (2009) Genetic characterization of a new astrovirus detected in dogs suffering from diarrhoea. Vet Microbiol 139: 147-152.
53. Moser LA, Schultz-Cherry S, (2005) Pathogenesis of astrovirus infection. Viral Immunol 18: 4-10.
54. Pantin-Jackwood MJ, Spackman E, Woolcock PR, (2006) Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: implications for diagnostics. Avian Dis 50: 397-404.
55. Monceyron JC, (2006) SARS/avian coronaviruses. Dev Biol (Basel) 126: 161-169.
56. Chetverin AB, Chetverina HV, Demidenko AA, Ugarov VI, (1997) Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure. Cell 88: 503-513.
57. Gmyl AP, Korshenko SA, Belousov EV, Khitrina EV, Agol VI, (2003) Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9: 1221-1231.
58. Gallei A, Pankraz A, Thiel HJ, Becher P, (2004) RNA recombination in vivo in the absence of viral replication. J Virol 78: 6271-6281.
59. Quan PL, Firth C, Street C, Henriquez JA, Petrosov A, et al. (2010) Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. Mbio 1 (Issue 4): 1-9.