Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

Journal of General Virology

Volumn 94, Issue PART 11, 2013, Pages 2480-2488

  Chouhy, Diego ^a,b   Bolatti, Elisa M ^b   Pérez, Germán R ^a,b   Giri, Adriana A ^a,b  

^a UNIVERSIDAD NACIONAL DE ROSARIO   (Argentina)

^b Instituto de Biologia Molecular y Celular de Rosario   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHAPAPILLOMAVIRUS; AMPLICON; ARTICLE; BETAPAPILLOMAVIRUS; GAMMAPAPILLOMAVIRUS; GENE SEQUENCE; GENETIC VARIABILITY; GENUS; MUPAPILLOMAVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; NUPAPILLOMAVIRUS; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TAXONOMIC IDENTIFICATION; UNINDEXED SEQUENCE; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN; VIRUS TYPING; WART VIRUS;

ALPHAPAPILLOMAVIRUS; BETAPAPILLOMAVIRUS; CAPSID PROTEINS; DNA PRIMERS; DNA, VIRAL; GAMMAPAPILLOMAVIRUS; GENETIC VARIATION; GENOME, VIRAL; HUMANS; MUPAPILLOMAVIRUS; ONCOGENE PROTEINS, VIRAL; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84885669893     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.055137-0     Document Type: Article

References (32)

1. Antonsson, A., Forslund, O., Ekberg, H., Sterner, G. & Hansson, B. G. (2000). The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses. J Virol 74, 11636-11641.
2. Asgari, M. M., Kiviat, N. B., Critchlow, C. W., Stern, J. E., Argenyi, Z. B., Raugi, G. J., Berg, D., Odland, P. B., Hawes, S. E. & de Villiers, E. M. (2008). Detection of human papillomavirus DNA in cutaneous squamous cell carcinoma among immunocompetent individuals. J Invest Dermatol 128, 1409-1417.
3. Berkhout, R. J., Bouwes Bavinck, J. N. & ter Schegget, J. (2000). Persistence of human papillomavirus DNA in benign and (pre)-malignant skin lesions from renal transplant recipients. J Clin Microbiol 38, 2087-2096.
4. Bernard, H. U., Burk, R. D., Chen, Z., van Doorslaer, K., zur Hausen, H. & de Villiers, E. M. (2010). Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 401, 70-79.
5. Bottalico, D., Chen, Z., Dunne, A., Ostoloza, J., McKinney, S., Sun, C., Schlecht, N. F., Fatahzadeh, M., Herrero, R. & other authors (2011). The oral cavity contains abundant known and novel human papillomaviruses from the Betapapillomavirus and Gammapapillomavirus genera. J Infect Dis 204, 787-792.
6. Chen, A. C., McMillan, N. A. & Antonsson, A. (2008). Human papillomavirus type spectrum in normal skin of individuals with or without a history of frequent sun exposure. J Gen Virol 89, 2891-2897.
7. Chouhy, D., Gorosito, M., Sánchez, A., Serra, E. C., Bergero, A., Fernandez Bussy, R. & Giri, A. A. (2010). New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3. Virology 397, 205-216.
8. Chouhy, D., Bolatti, E. M., Piccirilli, G., Sánchez, A., Fernandez Bussy, R. & Giri, A. A. (2013). Identification of human papillomavirus type 156, the prototype of a new human gammapapillomavirus species, by a generic and highly sensitive PCR strategy for long DNA fragments. J Gen Virol 94, 524-533.
9. de Villiers, E. M. (2013). Cross-roads in the classification of papillomaviruses. Virology [Epub ahead of print]
10. de Villiers, E. M., Fauquet, C., Broker, T. R., Bernard, H. U. & zur Hausen, H. (2004). Classification of papillomaviruses. Virology 324, 17-27.
11. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29, 1969-1973.
12. Forslund, O. (2007). Genetic diversity of cutaneous human papillomaviruses. J Gen Virol 88, 2662-2669.
13. Forslund, O., Antonsson, A., Nordin, P., Stenquist, B. & Hansson, B. G. (1999). 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 80, 2437-2443.
14. Forslund, O., Ly, H. & Higgins, G. (2003). Improved detection of cutaneous human papillomavirus DNA by single tube nested 'hanging droplet' PCR. J Virol Methods 110, 129-136.
15. Forslund, O., Iftner, T., Andersson, K., Lindelof, B., Hradil, E., Nordin, P., Stenquist, B., Kirnbauer, R., Dillner, J., de Villiers, E. M. & Viraskin Study Group (2007). Cutaneous human papillomaviruses found in sun-exposed skin: Beta-papillomavirus species 2 predominates in squamous cell carcinoma. J Infect Dis 196, 876-883.
16. Gottschling, M., Göker, M., Stamatakis, A., Bininda-Emonds, O. R., Nindl, I. & Bravo, I. G. (2011). Quantifying the phylodynamic forces driving papillomavirus evolution. Mol Biol Evol 28, 2101-2113.
17. Harwood, C. A., Surentheran, T., McGregor, J. M., Spink, P. J., Leigh, I. M., Breuer, J. & Proby, C. M. (2000). Human papillomavirus infection and non-melanoma skin cancer in immunosuppressed and immunocompetent individuals. J Med Virol 61, 289-297.
18. Harwood, C. A., Surentheran, T., Sasieni, P., Proby, C. M., Bordea, C., Leigh, I. M., Wojnarowska, F., Breuer, J. & McGregor, J. M. (2004). Increased risk of skin cancer associated with the presence of epidermodysplasia verruciformis human papillomavirus types in normal skin. Br J Dermatol 150, 949-957.
19. Hazard, K., Andersson, K., Dillner, J. & Forslund, O. (2007a). Human papillomavirus subtypes are not uncommon. Virology 362, 6-9.
20. Hazard, K., Karlsson, A., Andersson, K., Ekberg, H., Dillner, J. & Forslund, O. (2007b). Cutaneous human papillomaviruses persist on healthy skin. J Invest Dermatol 127, 116-119.
21. Hedtke, S. M., Townsend, T. M. & Hillis, D. M. (2006). Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst Biol 55, 522-529.
22. Kocjan, B. J., Jelen, M. M., Maver, P. J., Seme, K. & Poljak, M. (2011). Pre-vaccination genomic diversity of human papillomavirus genotype 6 (HPV 6): a comparative analysis of 21 full-length genome sequences. Infect Genet Evol 11, 1805-1810.
23. Manos, M. M., Ting, Y., Wright, D. K., Lewis, A. J., Broker, T. R. & Wolinski, S. M. (1989). Use of polymerase chain reaction amplification for the detection of genital human papillomaviruses. Cancer Cells 7, 209-214.
24. Menzo, S., Monachetti, A., Trozzi, C., Ciavattini, A., Carloni, G., Varaldo, P. E. & Clementi, M. (2001). Identification of six putative novel human papillomaviruses (HPV) and characterization of candidate HPV type 87. J Virol 75, 11913-11919.
25. Narechania, A., Chen, Z., DeSalle, R. & Burk, R. D. (2005). Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol 79, 15503-15510.
26. Peyton, C. L. & Wheeler, C. M. (1994). Identification of five novel human papillomavirus sequences in the New Mexico triethnic population. J Infect Dis 170, 1089-1092.
27. Pfister, H., Fuchs, P. G., Majewski, S., Jablonska, S., Pniewska, I. & Malejczyk, M. (2003). High prevalence of epidermodysplasia verruciformis-associated human papillomavirus DNA in actinic keratoses of the immunocompetent population. Arch Dermatol Res 295, 273-279.
28. Shamanin, V., Glover, M., Rausch, C., Proby, C., Leigh, I. M., zur Hausen, H. & de Villiers, E. M. (1994). Specific types of human papillomavirus found in benign proliferations and carcinomas of the skin in immunosuppressed patients. Cancer Res 54, 4610-4613.
29. Shamanin, V., zur Hausen, H., Lavergne, D., Proby, C. M., Leigh, I. M., Neumann, C., Hamm, H., Goos, M., Haustein, U. F. & other authors (1996). Human papillomavirus infections in nonmelanoma skin cancers from renal transplant recipients and nonimmunosuppressed patients. J Natl Cancer Inst 88, 802-811.
30. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
31. Varsani, A., van der Walt, E., Heath, L., Rybicki, E. P., Williamson, A. L. & Martin, D. P. (2006). Evidence of ancient papillomavirus recombination. J Gen Virol 87, 2527-2531.
32. Zwickl, D. J. & Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 51, 588-598.