Analysis of HPV

Persistent infection of oncogenic HPV types is acknowledged as a major risk factor for the development of cervical carcinoma [1-2]. Most of these high-risk types are phylogenetically clustered with Human papillomavirus 16 or Human papillomavirus 18 [3].  According to Bernard et al. [4] the classification of the family Papillomaviridae has been expanded and contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non human mammals, birds and reptiles (64, 3 and 2 types respectively). According to de Villiers et al. [5] genomic sequence similarities are used for their definitions to types, subtypes and variants. Isolates which differ within the same type by 2 to 10%, compared to prototype, are classified as subtypes, while isolates are classified as variants when they differ from 0-2% from the prototype. HPV types 16, 31, 33 belong to species 9 and HPV types 18, 45 belong to species 7 [5]. The ICTV has not set standards for the definition of taxonomic levels lower than species. Chen et al.[6-7] define variants of the same type as distinct lineages, when there is an approximate cut off of 1% difference between genomes and differences between genomes in 0.5%-1% range are designated as sublineages. Analysis of HPV variants diversity worldwide is of great importance as the HPV sequence data bases created, are useful for epidemiological and evolutionary studies, for the development of accurate diagnostic tests and for efficient vaccine design.

1.     Li, N.; Franceschi, S.; Howell-Jones, R.; Snijders, P.J.; Clifford, G.M. Human papillomavirus type distribution in 30,848 invasive cervical cancers worldwide: Variation by geographical region, histological type and year of publication. Int J Cancer 2011, 128, 927-935.

2.     Munoz, N.; Bosch, F.X.; de Sanjose, S.; Herrero, R.; Castellsague, X.; Shah, K.V.; Snijders, P.J.; Meijer, C.J. Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med 2003, 348, 518-527.

3.     Schiffman, M.; Herrero, R.; Desalle, R.; Hildesheim, A.; Wacholder, S.; Rodriguez, A.C.; Bratti, M.C.; Sherman, M.E.; Morales, J.; Guillen, D., et al. The carcinogenicity of human papillomavirus types reflects viral evolution. Virology 2005, 337, 76-84.

4.     Bernard, H.U.; Burk, R.D.; Chen, Z.; van Doorslaer, K.; Hausen, H.; de Villiers, E.M. Classification of papillomaviruses (pvs) based on 189 pv types and proposal of taxonomic amendments. Virology 2010, 401, 70-79.

5.     de Villiers, E.M.; Fauquet, C.; Broker, T.R.; Bernard, H.U.; zur Hausen, H. Classification of papillomaviruses. Virology 2004, 324, 17-27.

6.     Chen, Z.; DeSalle, R.; Schiffman, M.; Herrero, R.; Burk, R.D. Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol 2009, 83, 1443-1455.

7.     Chen, Z.; Schiffman, M.; Herrero, R.; Desalle, R.; Anastos, K.; Segondy, M.; Sahasrabuddhe, V.V.; Gravitt, P.E.; Hsing, A.W.; Burk, R.D. Evolution and taxonomic classification of human papillomavirus 16 (hpv16)-related variant genomes: Hpv31, hpv33, hpv35, hpv52, hpv58 and hpv67. PLoS One 2011, 6, e20183.

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