Genomic sequencing of a virus representing a novel type within the species Dyopipapillomavirus 1 in an Indian River Lagoon bottlenose dolphin

  • Galaxia Cortés-Hinojosa
  • Kuttichantran Subramaniam
  • James F. X. WellehanJr.
  • Terry Fei Fan Ng
  • Eric Delwart
  • Stephen D. McCulloch
  • Juli D. Goldstein
  • Adam M. Schaefer
  • Patricia A. Fair
  • John S. Reif
  • Gregory D. Bossart
  • Thomas B. WaltzekEmail author
Original Article


Fecal samples collected from free-ranging Atlantic bottlenose dolphins (BDs) in the Indian River Lagoon of Florida were processed for viral discovery using a next-generation sequencing (NGS) approach. A 693-bp contig identified in the NGS data was nearly identical to the partial L1 gene sequence of a papillomavirus (PV) previously found in a penile papilloma in a killer whale (Orcinus orca). Based on this partial bottlenose dolphin papillomavirus (BDPV) sequence, a nested inverse PCR and primer-walking strategy was employed to generate the complete genome sequence. The full BDPV genome consisted of 7299 bp and displayed a typical PV genome organization. The BDPV E6 protein contained a PDZ-binding motif, which has been shown to be involved in carcinogenic transformation involving high-risk genital human PVs. Screening of 12 individual fecal samples using a specific endpoint PCR assay revealed that the feces from a single female BD displaying a genital papilloma was positive for the BDPV. Genetic analysis indicated that this BDPV (Tursiops truncatus papillomavirus 8; TtPV8) is a new type of Dyopipapillomavirus 1, previously sequenced from an isolate obtained from a penile papilloma in a harbor porpoise (Phocoena phocoena). Although only a partial L1 sequence has been determined for a PV detected in a killer whale genital papilloma, our finding of a nearly identical sequence in an Atlantic BD may indicate that members of this viral species are capable of host jumping. Future work is needed to determine if this virus is a high-risk PV that is capable of inducing carcinogenic transformation and whether it poses a significant health risk to wild delphinid populations.



This study was partially funded by Florida Atlantic University (award no. 00086229), the Georgia Aquarium (award no. 03184), and the Florida Fish and Wildlife Conservation Commission (award no. 00126905).

Compliance with ethical standards

Conflict of interest

All the authors declare that they have no conflict of interest.

Ethical approval

All animal procedures were reviewed and approved by the Institutional Animal Care and Use Committee at the University of Florida (IACUC Protocol no. 201508900). BD samples used in this study were collected under US National Marine Fisheries Service Scientific Research Permit no. 14352.

Supplementary material

705_2018_4117_MOESM1_ESM.pdf (823 kb)
Fig. S1 Genetic comparison of the L1 gene of a novel type of Dyopipapillomavirus 1 from a bottlenose dolphin (Tursiops truncatus papillomavirus 8; TtPV8) to those of representatives of 49 accepted type species in the family Papillomaviridae. Values are expressed as percent nucleotide sequence identity. See Table S3 for PV abbreviations. (PDF 823 kb)
705_2018_4117_MOESM2_ESM.doc (56 kb)
Supplementary material 2 (DOC 55 kb)
705_2018_4117_MOESM3_ESM.doc (54 kb)
Supplementary material 3 (DOC 54 kb)
705_2018_4117_MOESM4_ESM.doc (112 kb)
Supplementary material 4 (DOC 112 kb)


  1. 1.
    Bernard HU, Burk RD, DeVilliers EM, zur Hausen H (2012) Papillomaviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, New York, pp 235–248Google Scholar
  2. 2.
    Burk R, Chen Z, van Doorslaer K, Bernard H-U, Chan PKS, Desalle R, Dillner J, Forslund O, Haga T, McBride A, Villa LL (2015) ICTV taxonomic proposal 2015.014a-atD.A.v2.Papillomaviridae_10gen. Creation of 21 new species and 10 new genera in the family Papillomaviridae. Accessed 12 Dec 2017
  3. 3.
    Arbyn M, Tommasino M, Depuydt C, Dillner J (2014) Are 20 human papillomavirus types causing cervical cancer? J Pathol 234:431–435CrossRefGoogle Scholar
  4. 4.
    Han R, Cladel NM, Reed CA, Christensen ND (1998) Characterization of transformation function of cottontail rabbit papillomavirus E5 and E8 genes. Virology 251:253–263CrossRefGoogle Scholar
  5. 5.
    Bernard H-U, Burk RD, Chen Z, van Doorslaer K, Hz Hausen, de Villiers E-M (2010) Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 401:70–79CrossRefGoogle Scholar
  6. 6.
    de Villiers EM, Fauquet C, Broker TR, Bernard H-U, zur Hausen H (2004) Classification of papillomaviruses. Virology 324:17–27CrossRefGoogle Scholar
  7. 7.
    Robles-Sikisaka R, Rivera R, Nollens HH, St Leger J, Durden WN, Stolen M, Burchell J, Wellehan JF Jr (2012) Evidence of recombination and positive selection in cetacean papillomaviruses. Virology 427:189–197CrossRefGoogle Scholar
  8. 8.
    Otten N, von Tscharner C, Lazary S, Antczak D, Gerber H (1993) DNA of bovine papillomavirus type 1 and 2 in equine sarcoids: PCR detection and direct sequencing. Arch Virol 132:121–131CrossRefGoogle Scholar
  9. 9.
    Munday JS, Thomson N, Dunowska M, Knight CG, Laurie RE, Hills S (2015) Genomic characterisation of the feline sarcoid-associated papillomavirus and proposed classification as Bos taurus papillomavirus type 14. Vet Microbiol 177:289–295CrossRefGoogle Scholar
  10. 10.
    Halvorsen KM, Keith EO (2008) Immunosuppression cascade in the Florida manatee (Trichechus manatus latirostris). Aquat Mamm 34:412–419CrossRefGoogle Scholar
  11. 11.
    Rector A, Bossart GD, Ghim SJ, Sundberg JP, Jenson AB, Van Ranst M (2004) 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 78:12698–12702CrossRefGoogle Scholar
  12. 12.
    Bossart GD, Ewing RY, Lowe M, Sweat M, Decker SJ, Walsh CJ, Ghim SJ, Jenson AB (2002) Viral papillomatosis in Florida manatees (Trichechus manatus latirostris). Exp Mol Pathol 72:37–48CrossRefGoogle Scholar
  13. 13.
    Ghim SJ, Joh J, Mignucci-Giannoni AA, Rivera-Guzmán AL, Falcón-Matos L, Alsina-Guerrero MM, Rodríguez-Villanueva M, Jenson AB, Bossart GD (2015) Genital papillomatosis associated with two novel mucosotropic papillomaviruses from a Florida manatee (Trichechus manatus latirostris). Aquat Mamm 40:195–200CrossRefGoogle Scholar
  14. 14.
    Gottschling M, Bravo IG, Schulz E, Bracho MA, Deaville R, Jepson PD, Van Bressem MF, Stockfleth E, Nindl I (2011) Modular organizations of novel cetacean papillomaviruses. Mol Phylogenet Evol 59:34–42CrossRefGoogle Scholar
  15. 15.
    De Guise S, Lagacé A, Béland P (1994) Gastric papillomas in eight St. Lawrence beluga whales (Delphinapterus leucas). J Vet Diagn Investig 6:385–388CrossRefGoogle Scholar
  16. 16.
    Van Bressem M, Van Waerebeek K, Raga J (1999) A review of virus infections of cetaceans and the potential impact of morbilliviruses, poxviruses and papillomaviruses on host population dynamics. Dis Aquat Org 38:53–65CrossRefGoogle Scholar
  17. 17.
    Rehtanz M, Ghim SJ, Rector A, Van Ranst M, Fair PA, Bossart GD, Jenson AB (2006) Isolation and characterization of the first American bottlenose dolphin papillomavirus: Tursiops truncatus papillomavirus type 2. J Gen Virol 87:3559–3565CrossRefGoogle Scholar
  18. 18.
    Van Bressem M, Kastelein R, Flamant P, Orth G (1999) Cutaneous papillomavirus infection in a harbour porpoise (Phocoena phocoena) from the North Sea. Vet Rec 144:592–593CrossRefGoogle Scholar
  19. 19.
    Van Bressem MF, Cassonnet P, Rector A, Desaintes C, Van Waerebeek K, Alfaro-Shigueto J, Van Ranst M, Orth G (2007) 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 88:1928–1933CrossRefGoogle Scholar
  20. 20.
    Stevens H, Rector A, Bertelsen MF, Leifsson PS, Van Ranst M (2008) Novel papillomavirus isolated from the oral mucosa of a polar bear does not cluster with other papillomaviruses of carnivores. Vet Microbiol 129:108–116CrossRefGoogle Scholar
  21. 21.
    Ng TFF, Miller MA, Kondov NO, Dodd EM, Batac F, Manzer M, Ives S, Saliki JT, Deng X, Delwart E (2015) Oral papillomatosis caused by Enhydra lutris papillomavirus 1 (Elpv-1) in southern sea otters (Enhydra lutris nereis) in California, USA. J Wildl Dis 51:446–453CrossRefGoogle Scholar
  22. 22.
    Rivera R, Robles-Sikisaka R, Hoffman E, Stacy BA, Jensen ED, Nollens HH, Wellehan JF Jr (2012) Characterization of a novel papillomavirus species (ZcPV1) from two California sea lions (Zalophus californianus). Vet Microbiol 155:257–266CrossRefGoogle Scholar
  23. 23.
    Rector A, Stevens H, Lacave G, Lemey P, Mostmans S, Salbany A, Vos M, Van Doorslaer K, Ghim SJ, Rehtanz M, Bossart GD, Jenson AB, Van Ranst M (2008) Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae. Virology 378:151–161CrossRefGoogle Scholar
  24. 24.
    Bossart GD, Ghim SJ, Rehtanz M, Goldstein J, Varela R, Ewing R, Fair P (2005) Orogenital neoplasia in Atlantic bottlenose dolphins (Tursiops truncatus). Aquat Mamm 31:473–480CrossRefGoogle Scholar
  25. 25.
    Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E (2014) Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci 111:16842–16847CrossRefGoogle Scholar
  26. 26.
    Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (2012) High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol 86:12161–12175CrossRefGoogle Scholar
  27. 27.
    Ng TF, Kondov NO, Deng X, Van Eenennaam A, Neibergs HL, Delwart E (2015) A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol 89:5340–5349CrossRefGoogle Scholar
  28. 28.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  29. 29.
    Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277CrossRefGoogle Scholar
  30. 30.
    Abascal F, Zardoya R, Telford MJ (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res 38:W7–W13CrossRefGoogle Scholar
  31. 31.
    Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol 32:268–274CrossRefGoogle Scholar
  32. 32.
    McLaughlin-Drubin ME, Münger K (2009) Oncogenic activities of human papillomaviruses. Virus Res 143:195–208CrossRefGoogle Scholar
  33. 33.
    Ganti K, Broniarczyk J, Manoubi W, Massimi P, Mittal S, Pim D, Banks L (2015) The human papillomavirus E6 PDZ binding motif: from life cycle to malignancy. Viruses 7:3530–3551CrossRefGoogle Scholar
  34. 34.
    Smola-Hess S, Pfister H (2002) Interaction of papillomaviral oncoproteins with cellular factors. In: Holzenburg A, Dordrecht EB (eds) Structure-function relationships of human pathogenic viruses. Kluwer Academic, Norwell, pp 431–464CrossRefGoogle Scholar
  35. 35.
    Vilstrup JT, Ho SY, Foote AD, Morin PA, Kreb D, Krützen M, Parra GJ, Robertson KM, de Stephanis R, Verborgh P, Willerslev E, Orlando L, Gilbert MT (2011) Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol 11:1CrossRefGoogle Scholar
  36. 36.
    Van Doorslaer K (2013) Evolution of the Papillomaviridae. Virology 445:11–20CrossRefGoogle Scholar
  37. 37.
    Garcia-Perez R, Ibanez C, Godínez JM, Aréchiga N, Garin I, Pérez-Suárez G, de Paz O, Juste J, Echevarría JE, Bravo IG (2014) Novel papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity, and hints for recombination. Genome Biol Evol 6:94–104CrossRefGoogle Scholar
  38. 38.
    Garcia-Perez R, Gottschling M, Wibbelt G, Bravo I (2013) Multiple evolutionary origins of bat papillomaviruses. Vet Microbiol 165:51–60CrossRefGoogle Scholar
  39. 39.
    Herzing DL, Elliser CR (2013) Directionality of sexual activities during mixed-species encounters between Atlantic spotted dolphins (Stenella frontalis) and bottlenose dolphins (Tursiops truncatus). Int J Comp Psychol 26:124–134Google Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Small Animal Clinical Sciences, College of Veterinary MedicineUniversity of FloridaGainesvilleUSA
  2. 2.Department of Infectious Diseases and Immunology, College of Veterinary MedicineUniversity of FloridaGainesvilleUSA
  3. 3.Department of Comparative, Diagnostic and Population Medicine, College of Veterinary MedicineUniversity of FloridaGainesvilleUSA
  4. 4.College of Veterinary MedicineUniversity of GeorgiaAthensUSA
  5. 5.Blood Systems Research InstituteSan FranciscoUSA
  6. 6.Department of Laboratory MedicineUniversity of California at San FranciscoSan FranciscoUSA
  7. 7.Division of Marine Mammal Research and Conservation, Center of Marine Ecosystems Health, Harbor Branch Oceanographic InstitutionFlorida Atlantic UniversityFort PierceUSA
  8. 8.Protect Wild Dolphins AllianceVero BeachUSA
  9. 9.National Oceanic and Atmospheric Administration, National Ocean ServiceCenter for Coastal Environmental Health and Biomolecular ResearchCharlestonUSA
  10. 10.Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical SciencesColorado State UniversityFort CollinsUSA
  11. 11.Georgia AquariumAtlantaUSA
  12. 12.Division of Comparative Pathology, Miller School of MedicineUniversity of MiamiMiamiUSA

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