1887

Journal of General Virology header logo

Volume 99, Issue 12

Genomic characterization of Erethizon dorsatum papillomavirus 2, a new papillomavirus species marked by its exceptional genome size Free

Abstract

We report here the complete sequence and genome organization of a new papillomavirus, Erethizon dorsatum papillomavirus 2 (EdPV2), which was isolated from cutaneous lesions observed on the muzzle of a North American porcupine. The complete genome is 8809 nucleotides long and encodes five early (E6-E7-E1-E2-E4) and two late proteins (L2-L1). In addition to the upstream regulatory region, the EdPV2 genome contains an exceptionally large secondary non-coding region with no apparent functional relevance. EdPV2 is strongly divergent from the previously described porcupine papillomavirus EdPV1 and phylogenetic analysis shows EdPV2 clustering near members of the genus Pipapillomavirus, a group of rodent papillomaviruses. Pairwise sequence comparison based on the L1 open reading frame identifies Rattus norvegicus papillomavirus 1 as the closest related virus (59.97 % similarity). Based on its low sequence similarity to other known papillomaviruses, EdPV2 is thought to represent a new genus in the family Papillomaviridae.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): EdPV2 , Erethizon dorsatum papillomavirus 2 , North American porcupine and Papillomavirus
© 2018 The Authors
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001164
2018-10-24
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/jgv/99/12/1699.html?itemId=/content/journal/jgv/10.1099/jgv.0.001164&mimeType=html&fmt=ahah

References

  1. PaVE Papillomavirus Episteme. Available from https://pave.niaid.nih.gov [accessed 20 April 20 2018]
  2. van Doorslaer K, Li Z, Xirasagar S, Maes P, Kaminsky D et al. The papillomavirus episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res 2017; 45:D499–D506 [View Article][PubMed]
     [Google Scholar]
  3. Delius H, van Ranst MA, Jenson AB, Zur Hausen H, Sundberg JP. Canine oral papillomavirus genomic sequence: a unique 1.5-kb intervening sequence between the E2 and L2 open reading frames. Virology 1994; 204:447–452 [View Article][PubMed]
     [Google Scholar]
  4. López-Bueno A, Mavian C, Labella AM, Castro D, Borrego JJ et al. Concurrence of iridovirus, polyomavirus, and a unique member of a new group of fish papillomaviruses in lymphocystis disease-affected gilthead sea bream. J Virol 2016; 90:8768–8779 [View Article][PubMed]
     [Google Scholar]
  5. van Doorslaer K. Evolution of the papillomaviridae. Virology 2013; 445:11–20 [View Article][PubMed]
     [Google Scholar]
  6. Zheng ZM, Baker CC. Papillomavirus genome structure, expression, and post-transcriptional regulation. Front Biosci 2006; 11:2286–2302 [View Article][PubMed]
     [Google Scholar]
  7. Bernard HU. Regulatory elements in the viral genome. Virology 2013; 445:197–204 [View Article][PubMed]
     [Google Scholar]
  8. Munday JS. Bovine and human papillomaviruses: a comparative review. Vet Pathol 2014; 51:1063–1075 [View Article][PubMed]
     [Google Scholar]
  9. Rector A, van Ranst M. Animal papillomaviruses. Virology 2013; 445:213–223 [View Article][PubMed]
     [Google Scholar]
  10. Angulo M, Carvajal-Rodríguez A. Evidence of recombination within human alpha-papillomavirus. Virol J 2007; 4:33 [View Article][PubMed]
     [Google Scholar]
  11. Gottschling M, Göker M, Stamatakis A, Bininda-Emonds OR, Nindl I et al. Quantifying the phylodynamic forces driving papillomavirus evolution. Mol Biol Evol 2011; 28:2101–2113 [View Article][PubMed]
     [Google Scholar]
  12. Rector A, Tachezy R, van Doorslaer K, Macnamara T, Burk RD et al. Isolation and cloning of a papillomavirus from a North American porcupine by using multiply primed rolling-circle amplification: the Erethizon dorsatum papillomavirus type 1. Virology 2005; 331:449–456 [View Article][PubMed]
     [Google Scholar]
  13. Schwartz S, Lockwood SL, Sledge D, Maes RK, Wise AG. Diagnosis and treatment of a novel papillomavirus in a North American porcupine (Erethizon dorsatum). Vet Rec Case Rep 2018; 6:e000609 [View Article]
     [Google Scholar]
  14. Manos MM, Ting Y, Wright DK, Lewis AJ, Broker TR et al. Use of polymerase chain-reaction amplification for the detection of genital human papillomaviruses. Cancer Cel 1989; 7:209
     [Google Scholar]
  15. Forslund O, Antonsson A, Nordin P, Stenquist B, Hansson BG. A broad range of human papillomavirus types detected with a general PCR method suitable for analysis of cutaneous tumours and normal skin. J Gen Virol 1999; 80:2437–2443 [View Article][PubMed]
     [Google Scholar]
  16. Rector A, Bossart GD, Ghim SJ, Sundberg JP, Jenson AB et al. 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 2004; 78:12698–12702 [View Article][PubMed]
     [Google Scholar]
  17. Roman A, Munger K. The papillomavirus E7 proteins. Virology 2013; 445:138–168 [View Article][PubMed]
     [Google Scholar]
  18. vande Pol SB, Klingelhutz AJ. Papillomavirus E6 oncoproteins. Virology 2013; 445:115–137 [View Article][PubMed]
     [Google Scholar]
  19. Dahiya A, Gavin MR, Luo RX, Dean DC. Role of the LXCXE binding site in Rb function. Mol Cell Biol 2000; 20:6799–6805 [View Article][PubMed]
     [Google Scholar]
  20. Bergvall M, Melendy T, Archambault J. The E1 proteins. Virology 2013; 445:35–56 [View Article][PubMed]
     [Google Scholar]
  21. McBride AA. The papillomavirus E2 proteins. Virology 2013; 445:57–79 [View Article][PubMed]
     [Google Scholar]
  22. Doorbar J. The E4 protein; structure, function and patterns of expression. Virology 2013; 445:80–98 [View Article][PubMed]
     [Google Scholar]
  23. Fay A, Yutzy WH, Roden RB, Moroianu J. The positively charged termini of L2 minor capsid protein required for bovine papillomavirus infection function separately in nuclear import and DNA binding. J Virol 2004; 78:13447–13454 [View Article][PubMed]
     [Google Scholar]
  24. Zhou J, Doorbar J, Sun XY, Crawford LV, Mclean CS et al. Identification of the nuclear localization signal of human papillomavirus type 16 L1 protein. Virology 1991; 185:625–632 [View Article][PubMed]
     [Google Scholar]
  25. Chen G, Stenlund A. Characterization of the DNA-binding domain of the bovine papillomavirus replication initiator E1. J Virol 1998; 72:2567–2576[PubMed]
     [Google Scholar]
  26. Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA 2012; 3:385–396 [View Article][PubMed]
     [Google Scholar]
  27. García-Pérez R, Ibáñez C, Godínez JM, Aréchiga N, Garin I et al. Novel papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity, and hints for recombination. Genome Biol Evol 2014; 6:94–104 [View Article][PubMed]
     [Google Scholar]
  28. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
     [Google Scholar]
  29. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014; 10:e1003537 [View Article][PubMed]
     [Google Scholar]
  30. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001; 18:691–699 [View Article][PubMed]
     [Google Scholar]
  31. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
     [Google Scholar]
  32. Shah SD, Doorbar J, Goldstein RA. Analysis of host-parasite incongruence in papillomavirus evolution using importance sampling. Mol Biol Evol 2010; 27:1301–1314 [View Article][PubMed]
     [Google Scholar]
  33. de Villiers EM, Fauquet C, Broker TR, Bernard HU, Zur Hausen H. Classification of papillomaviruses. Virology 2004; 324:17–27 [View Article][PubMed]
     [Google Scholar]
  34. van Doorslaer K, Chen Z, Bernard HU, Chan PKS, Desalle R et al. ICTV virus taxonomy profile: Papillomaviridae. J Gen Virol 2018; 99:989–990 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001164
Loading
Genomic characterization of Erethizon dorsatum papillomavirus 2, a new papillomavirus species marked by its exceptional genome size
J. Gen. Virol. 99, 1699 (2018); https://doi.org/10.1099/jgv.0.001164
/content/journal/jgv/10.1099/jgv.0.001164
/content/journal/jgv/10.1099/jgv.0.001164
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error