Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae

Virology

Volumn 378, Issue 1, 2008, Pages 151-161

  Rector, Annabel ^a   Stevens, Hans ^a   Lacave, Géraldine ^b,c   Lemey, Philippe ^a,d   Mostmans, Sara ^a   Salbany, Ana ^c   Vos, Melissa ^a   Van Doorslaer, Koenraad ^a   Ghim, Shin Je ^e   Rehtanz, Manuela ^e,f   Bossart, Gregory D ^f,g   Jenson, A Bennett ^e   Van Ranst, Marc ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b Marine Mammal Veterinary Services   (Belgium)

^c Mundo Aquatico Zoomarine ^*  (Portugal)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e UNIVERSITY OF LOUISVILLE   (United States)

^f FLORIDA ATLANTIC UNIVERSITY   (United States)

^g FLORIDA ATLANTIC UNIVERSITY   (United States)

Author keywords

Bootscanning; Bottlenose dolphin (Tursiops truncatus); Cetacea; Condylomata; Evolution; Papillomaviridae; Phylogeny; Recombination; Selection

Indexed keywords

ANALYTIC METHOD; ARTICLE; BOTTLENOSE DOLPHIN; CODON; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; GENETIC RECOMBINATION; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PHYLOGENY; PRIORITY JOURNAL; VIRUS GENOME;

ANIMALS; CONDYLOMATA ACUMINATA; DOLPHINS; EVOLUTION, MOLECULAR; FEMALE; GENITALIA, FEMALE; GENITALIA, MALE; GENOME, VIRAL; MALE; MOLECULAR SEQUENCE DATA; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; PHOCOENA; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

CETACEA; PAPILLOMAVIRIDAE; PHOCOENA SPINIPINNIS; TURSIOPS; TURSIOPS TRUNCATUS;

EID: 47949115752     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2008.05.020     Document Type: Article

References (51)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Angulo M., and Carvajal-Rodriguez A. Evidence of recombination within human alpha-papillomavirus. J. Virol. 4 (2007) 33
3. Antonsson A., and Hansson B.G. Healthy skin of many animal species harbors papillomaviruses which are closely related to their human counterparts. J. Virol. 76 (2002) 12537-12542
4. Bossart G.D., Cray C., Solorzano J.L., Decker S.J., Cornell L.H., and Altman N.H. Cutaneous papillomaviral-like papillomatosis in a killer whale (Orcinus orca). Marine Mamm. Sci. 12 (1996) 274-281
5. Bossart G.D., Ghim S.J., Rehtanz M., Goldstein J.D., Varela R.A., Ewing R.Y., Fair P.A., Lenzi R., Joseph B., Hicks C., Schneider L., McKinnie C.J., Reif J.S., Sanchez R., Lopez A., Novoa S., Bernal J., Goretti M., Rodriguez M., Defran R.H., and Jenson A.B. Orogenital neoplasia in Atlantic bottlenose dolphins (Tursiops truncatus). Aquat. Mamm. 31 (2005) 473-480
6. Bravo I.G., and Alonso A. Mucosal human papillomaviruses encode four different E5 proteins whose chemistry and phylogeny correlate with malignant or benign growth. J. Virol. 78 (2004) 13613-13626
7. Bravo I.G., and Alonso A. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins. Virus Genes 34 (2007) 249-262
8. Chan S.Y., Bernard H.U., Ratterree M., Birkebak T.A., Faras A.J., and Ostrow R.S. Genomic diversity and evolution of papillomaviruses in rhesus monkeys. J. Virol. 71 (1997) 4938-4943
9. De Guise S., Lagace A., and Beland P. Gastric papillomas in eight St. Lawrence beluga whales (Delphinapterus leucas). J. Vet. Diagn. Invest. 6 (1994) 385-388
10. de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U., and zur Hausen H. Classification of papillomaviruses. Virology 324 (2004) 17-27
11. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
12. Flom J.O., Brown R.J., Jones R.E., and Schonewald J. Vaginal fibromas in a beaked whale, Mesoplodon densirostris. J. Wildl. Dis. 16 (1980) 99-102
13. Garcia-Vallve S., Alonso A., and Bravo I.G. Papillomaviruses: different genes have different histories. Trends Microbiol. 13 (2005) 514-521
14. Gardiol D., Kuhne C., Glaunsinger B., Lee S.S., Javier R., and Banks L. Oncogenic human papillomavirus E6 proteins target the discs large tumour suppressor for proteasome-mediated degradation. Oncogene 18 (1999) 5487-5496
15. Geraci J.R., Palmer N.C., and St. Aubin D.J. Tumors in cetaceans: analysis and new findings. Can. J. Fish. Aquat. Sci. 44 (1987) 1289-1300
16. Gottschling M., Kohler A., Stockfleth E., and Nindl I. Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data. Mol. Phylogenet. Evol. 42 (2007) 213-222
17. Gottschling M., Stamatakis A., Nindl I., Stockfleth E., Alonso A., and Bravo I.G. Multiple evolutionary mechanisms drive papillomavirus diversification. Mol. Biol. Evol. 24 (2007) 1242-1258
18. Greenwood A.G., Harrison R.J., and Whitting H.W. Functional and pathological aspects of the skin of marine mammals. In: Harrison R.J. (Ed). Functional Anatomy of Marine Mammals (1974), Academic Press, London 73-110
19. Howley P.M., and Lowy D.R. Papillomaviruses and their replication. In: Knipe D.M., and Howley P.M. (Eds). Fields Virology (2001), Lippincott Williams & Wilkins, Philadelphia 2197-2229
20. Jing M., Bohl J., Brimer N., Kinter M., and Vande Pol S.B. Degradation of tyrosine phosphatase PTPN3 (PTPH1) by association with oncogenic human papillomavirus E6 proteins. J. Virol. 81 (2007) 2231-2239
21. Kiyono T., Hiraiwa A., Fujita M., Hayashi Y., Akiyama T., and Ishibashi M. Binding of high-risk human papillomavirus E6 oncoproteins to the human homologue of the Drosophila discs large tumor suppressor protein. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 11612-11616
22. Kosakovski Pond S.L., Frost S.D., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
23. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
24. Lambertsen R.H., Kohn B.A., Sundberg J.P., and Buergelt C.D. Genital papillomatosis in sperm whale bulls. J. Wildl. Dis. 23 (1987) 361-367
25. Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., and Ray S.C. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73 (1999) 152-160
26. Mendez F., Munoz N., Posso H., Molano M., Moreno V., van den Brule A.J., Ronderos M., Meijer C., and Munoz A. Cervical coinfection with human papillomavirus (HPV) types and possible implications for the prevention of cervical cancer by HPV vaccines. J. Infect. Dis. 192 (2005) 1158-1165
27. Narechania A., Chen Z., DeSalle R., and Burk R.D. Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J. Virol. 79 (2005) 15503-15510
28. Narechania A., Terai M., Chen Z., DeSalle R., and Burk R.D. Lack of the canonical pRB-binding domain in the E7 ORF of artiodactyl papillomaviruses is associated with the development of fibropapillomas. J. Gen. Virol. 85 (2004) 1243-1250
29. Nicholas K.B., Nicholas H.B., and Deerfield D.W. GeneDoc: analysis and visualization of genetic variation. Embnet News 4 (1997) 14
30. Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
31. Ogawa T., Tomita Y., Okada M., Shinozaki K., Kubonoya H., Kaiho I., and Shirasawa H. Broad-spectrum detection of papillomaviruses in bovine teat papillomas and healthy teat skin. J. Gen. Virol. 85 (2004) 2191-2197
32. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
33. Rector A., Bossart G.D., Ghim S.J., Sundberg J.P., Jenson A.B., and Van Ranst M. Characterization of a novel close-to-root papillomavirus from a Florida manatee by using multiply primed rolling-circle amplification: Trichechus manatus latirostris papillomavirus type 1. J. Virol. 78 (2004) 12698-12702
34. Rector A., Lemey P., Tachezy R., Mostmans S., Ghim S.J., Van Doorslaer K., Roelke M., Bush M., Montali R.J., Joslin J., Burk R.D., Jenson A.B., Sundberg J.P., Shapiro B., and Van Ranst M. Ancient papillomavirus-host co-speciation in Felidae. Genome Biol. 8 (2007) R57
35. Rector A., Tachezy R., and Van Ranst M. A sequence-independent strategy for detection and cloning of circular DNA virus genomes by using multiply primed rolling-circle amplification. J. Virol. 78 (2004) 4993-4998
36. Rehtanz M., Ghim S.J., Rector A., Van Ranst M., Fair P.A., Bossart G.D., and Jenson A.B. Isolation and characterization of the first American bottlenose dolphin papillomavirus: Tursiops truncatus papillomavirus type 2. J. Gen. Virol. 87 (2006) 3559-3565
37. 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. Retrovir. 11 (1995) 1423-1425
38. Sundberg J.P. Papillomavirus infections in animals. In: Syrjänen K., Gissmann L., and Koss L.G. (Eds). Papillomaviruses and Human Disease (1987), Springer-Verlag, Berlin 40-103
39. Sundberg J.P., Van Ranst M., Burk R.D., and Jenson A.B. The nonhuman (animal) papillomaviruses: host range, epitope conservation, and molecular diversity. In: Gross G., and von Krogh G. (Eds). Human papillomavirus infections in dermatovenereology (1997), CRC Press, Boca Raton 47-68
40. Swofford D.L. PAUP* 4.0 - Phylogenetic Analysis Using Parsimony (1998), Sinauer Associates, Sunderland
41. Syrjänen K.J., and Syrjänen S.M. Papillomavirus Infections in Human Pathology (2000), John Wiley and Sons Ltd, Chichester, West Sussex, UK
42. Tachezy R., Rector A., Havelkova M., Wollants E., Fiten P., Opdenakker G., Jenson B., Sundberg J., and Van Ranst M. Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV) genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus. BMC Microbiol. 2 (2002) 19-27
43. 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 (1994) 4673-4680
44. Van Bressem M.F., Cassonnet P., Rector A., Desaintes C., Van Waerebeek K., Alfaro-Shigueto J., Van Ranst M., and Orth G. Genital warts in Burmeister's porpoises: characterization of Phocoena spinipinnis papillomavirus type 1 (PsPV-1) and evidence for a second, distantly related PsPV. J. Gen. Virol. 88 (2007) 1928-1933
45. Van Bressem M.F., Kastelein R.A., Flamant P., and Orth G. Cutaneous papillomavirus infection in a harbour porpoise (Phocoena phocoena) from the North Sea. Vet. Rec. 144 (1999) 592-593
46. Van Bressem M.F., Van Waerebeek K., Piérard G.E., and Desaintes C. Genital and lingual warts in small cetaceans from coastal Peru. Dis. Aquat. Org. 26 (1996) 1-10
47. Van Ranst M., Kaplan J.B., and Burk R.D. Phylogenetic classification of human papillomaviruses: correlation with clinical manifestations. J. Gen. Virol. 73 (1992) 2653-2660
48. Varsani A., van der Walt E., Heath L., Rybicki E.P., Williamson A.L., and Martin D.P. Evidence of ancient papillomavirus recombination. J. Gen. Virol. 87 (2006) 2527-2531
49. Woolford L., Rector A., Van Ranst M., Ducki A., Bennett M.D., Nicholls P.K., Warren K.S., Swan R.A., Wilcox G.E., and O'Hara A.J. A novel virus detected in papillomas and carcinomas of the endangered western barred bandicoot (Perameles bougainville) exhibits genomic features of both the Papillomaviridae and Polyomaviridae. J. Virol. 81 (2007) 13280-13290
50. Xia X., and Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Heredity 92 (2001) 371-373
51. Yang Z., Nielsen R., Goldman N., and Pedersen A.M. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449