Human papillomavirus genomics: Past, present and future

Current Problems in Dermatology (Switzerland)

Volumn 45, Issue , 2014, Pages 1-18

  Harari, Ariana ^a   Chen, Zigui ^a   Burk, Robert D ^a,b,c  

^a Department of Microbiology and Immunology ^*  (United States)

^b Department of Obstetrics   (United States)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NEUTRALIZING ANTIBODY; NUCLEOTIDE; PROTEIN P53; RETINOBLASTOMA PROTEIN;

ALPHAPAPILLOMAVIRUS; CARCINOGENICITY; CELL TRANSFORMATION; DNA REPLICATION; DNA SEQUENCE; GENE EXPRESSION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; GENOTYPE; HUMAN PAPILLOMAVIRUS TYPE 16; HUMAN PAPILLOMAVIRUS TYPE 18; HUMAN PAPILLOMAVIRUS TYPE 31; HUMAN PAPILLOMAVIRUS TYPE 33; HUMAN PAPILLOMAVIRUS TYPE 35; HUMAN PAPILLOMAVIRUS TYPE 52; HUMAN PAPILLOMAVIRUS TYPE 58; MOLECULAR PATHOLOGY; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; POLYADENYLATION; PRECANCER; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; SKIN CARCINOMA; SPECIES; START CODON; TROPISM; UTERINE CERVIX CANCER; VIRUS CLASSIFICATION; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS LIKE AGENT; VIRUS REPLICATION; VIRUS TYPING; WART VIRUS; EVOLUTION; GENETIC VARIABILITY; GENETICS; HUMAN; PAPILLOMA VIRUS; UROGENITAL TRACT TUMOR; VIROLOGY;

BIOLOGICAL EVOLUTION; GENETIC VARIATION; GENOME, VIRAL; HUMANS; PAPILLOMAVIRIDAE; PHYLOGENY; UROGENITAL NEOPLASMS;

EID: 84920921122     PISSN: 14215721     EISSN: 16622944     Source Type: Book Series    
DOI: 10.1159/000355952     Document Type: Review

References (82)

1. De Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H: Classification of papillomaviruses. Virology 2004; 324: 17-27
2. Herbst LH, Lenz J, Van Doorslaer K, et al: Genomic characterization of two novel reptilian papillomaviruses, Chelonia mydas papillomavirus 1 and Caretta caretta papillomavirus 1. Virology 2009; 383: 131-135
3. Lange CE, Favrot C, Ackermann M, Gull J, Vetsch E, Tobler K: Novel snake papillomavirus does not cluster with other non-mammalian papillomaviruses. Virol J 2011; 8: 436
4. Bernard HU: Coevolution of papillomaviruses with human populations. Trends Microbiol 1994; 2: 140-143
5. Ho L, Chan SY, Burk RD, et al: The genetic drift of human papillomavirus type 16 is a means of reconstructing prehistoric viral spread and the movement of ancient human populations. J Virol 1993; 67: 6413-6423
6. Ong CK, Chan SY, Campo MS, et al: Evolution of human papillomavirus type 18: an ancient phylogenetic root in Africa and intratype diversity reflect coevolution with human ethnic groups. J Virol 1993; 67: 6424-6431
7. Zur Hausen H, de Villiers EM: Human papillomaviruses. Annu Rev Microbiol 1994; 48: 427-447
8. Burns DA: 'Warts and all'-the history and folklore of warts: A review. J R Soc Med 1992; 85: 37-40
9. Rigoni-Stern D: Fatti statistici relative alle mallatie cancrosi che servirono de base alla poche cose dette dal dott. Giornale service propr.pathol.terap.ser. 1842;2:507-517 [Italian]
10. Zur Hausen H: Papillomaviruses in the causation of human cancers-a brief historical account. Virology 2009;384:260-265
11. Schiffman M, Wentzensen N: Human papillomavirus infection and the multistage carcinogenesis of cervical cancer. Cancer Epidemiol Biomarkers Prev 2013; 22: 553-560
12. Schiffman M, Castle PE, Jeronimo J, Rodriguez AC, Wacholder S: Human papillomavirus and cervical cancer. Lancet 2007; 370: 890-907
13. Jemal A, Simard EP, Dorell C, et al: Annual report to the nation on the status of cancer, 1975-2009, featuring the burden and trends in human papillomavirus (HPV)-associated cancers and HPV vaccination coverage levels. J Natl Cancer Inst 2013; 105: 175-201
14. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D: Global cancer statistics. CA Cancer J Clin 2011; 61: 69-90
15. Shope RE, Hurst EW: Infectious papillomatosis of rabbits: with a note on the histopathology. J Exp Med 1933; 58: 607-624
16. Rous P, Beard JW: The progression to carcinoma of virus-induced rabbit papillomas (Shope). J Exp Med 1935; 62: 523-548
17. zur Hausen H: Human papillomaviruses and their possible role in squamous cell carcinomas. Curr Top Microbiol Immunol 1977;78:1-30
18. zur Hausen H: Papillomaviruses in anogenital cancer as a model to understand the role of viruses in human cancers. Cancer Res 1989;49:4677-4681
19. Bernard HU, Burk RD, Chen Z, van Doorslaer K, Hausen H, de Villiers EM: Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010; 401: 70-79
20. Munoz N, Bosch FX, de Sanjose S, et al: The causal link between human papillomavirus and invasive cervical cancer: A population-based case-control study in Colombia and Spain. Int J Cancer 1992; 52: 743-749
21. Rodriguez AC, Schiffman M, Herrero R, et al: Rapid clearance of human papillomavirus and implications for clinical focus on persistent infections. J Natl Cancer Inst 2008; 100: 513-517
22. Denny L, Kuhn L, Hu CC, Tsai WY, Wright TC Jr: Human papillomavirus-based cervical cancer prevention: long-term results of a randomized screening trial. J Natl Cancer Inst 2010; 102: 1557-1567
23. Barzon L, Militello V, Lavezzo E, et al: Human papillomavirus genotyping by 454 next generation sequencing technology. J Clin Virol 2011; 52: 93-97
24. Mighty KK, Laimins LA: The role of human papillomaviruses in oncogenesis. Recent Results Cancer Res 2014;193:135-148
25. Doorbar J, Quint W, Banks L, et al: The biology and life-cycle of human papillomaviruses. Vaccine 2012; 30: F55-F70
26. Johansson C, Schwartz S: Regulation of human papillomavirus gene expression by splicing and polyadenylation. Nat Rev Microbiol 2013; 11: 239-251
27. Chen Z, Schiffman M, Herrero R, et al: Evolution and taxonomic classification of human papillomavirus
28. (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PloS One 2011; 6:e20183
29. Klug A, Finch JT: Structure of viruses of the papilloma-polyoma type. I. Human wart virus. J Mol Biol 1965; 11: 403-423
30. Klug A, Finch JT: Structure of viruses of the papilloma-polyoma type. IV. Analysis of tilting experiments in the electron microscope. J Mol Biol 1968; 31: 1-12
31. Gissmann L, Pfister H, Zur Hausen H: Human papilloma viruses (HPV): characterization of four different isolates. Virology 1977; 76: 569-580
32. Reinson T, Toots M, Kadaja M, et al: Engagement of the ATR-dependent DNA damage response at the human papillomavirus 18 replication centers during the initial amplification. J Virol 2013; 87: 951-964
33. Phelps WC, Howley PM: Transcriptional trans-activation by the human papillomavirus type 16 E2 gene product. J of virol 1987;61:1630-1638
34. Bedrosian CL, Bastia D: The DNA-binding domain of HPV-16 E2 protein interaction with the viral enhancer: protein-induced DNA bending and role of the nonconserved core sequence in binding site affinity. Virology 1990;174:557-575
35. Hegde RS: The papillomavirus E2 proteins: structure, function, and biology. Annu Rev Biophys Biomol Struct 2002; 31: 343-360
36. Fu L, Van Doorslaer K, Chen Z, et al: Degradation of p53 by human Alphapapillomavirus E6 proteins shows a stronger correlation with phylogeny than oncogenicity. PloS One 2010; 5:e12816
37. Chen SL, Mounts P: Transforming activity of E5a protein of human papillomavirus type 6 in NIH 3T3 and C127 cells. J Virol 1990; 64: 3226-3233
38. Hwang ES, Nottoli T, Dimaio D: The HPV16 E5 protein: expression, detection, and stable complex formation with transmembrane proteins in COS cells. Virology 1995; 211: 227-233
39. Schiffman M, Herrero R, Desalle R, et al: The carcinogenicity of human papillomavirus types reflects viral evolution. Virology 2005; 337: 76-84
40. Zur Hausen H, Meinhof W, Scheiber W, Bornkamm GW: Attempts to detect virus-specific DNA in human tumors. I. Nucleic acid hybridizations with complementary RNA of human wart virus. Int J Cancer 1974; 13: 650-656
41. Boshart M, Gissmann L, Ikenberg H, Kleinheinz A, Scheurlen W, zur Hausen H: A new type of papillomavirus DNA, its presence in genital cancer biopsies and in cell lines derived from cervical cancer. EMBO J 1984; 3: 1151-1157
42. Van Ranst M, Fuse A, Sobis H, et al: A papillomavirus related to HPV type 13 in oral focal epithelial hyperplasia in the pygmy chimpanzee. J Oral Pathol Med 1991; 20: 325-331
43. Chan SY, Bernard HU, Ratterree M, Birkebak TA, Faras AJ, Ostrow RS: Genomic diversity and evolution of papillomaviruses in rhesus monkeys. J Virol 1997; 71: 4938-4943
44. Chen Z, van Doorslaer K, DeSalle R, et al: Genomic diversity and interspecies host infection of alpha12 Macaca fascicularis papillomaviruses (MfPVs). Virology 2009; 393: 304-310
45. Bergin IL, Bell JD, Chen Z, et al: Novel genital Alphapapillomaviruses in baboons (Papio hamadryas anubis) with cervical dysplasia. Vet Pathol 2013; 50: 200-208
46. Wood CE, Chen Z, Cline JM, Miller BE, Burk RD: Characterization and experimental transmission of an oncogenic papillomavirus in female macaques. J Virol 2007; 81: 6339-6345
47. Chen Z, DeSalle R, Schiffman M, Herrero R, Burk RD: Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol 2009; 83: 1443-1455
48. Rector A, Lemey P, Tachezy R, et al: Ancient papillomavirus-host co-speciation in Felidae. Genome Biol 2007; 8:R57
49. Narechania A, Chen Z, DeSalle R, Burk RD: Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol 2005; 79: 15503-15510
50. Burk RD, Chen Z, Van Doorslaer K: Human papillomaviruses: genetic basis of carcinogenicity. Public Health Genom 2009; 12: 281-290
51. Schiffman M, Rodriguez AC, Chen Z, et al: A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia. Cancer Res 2010; 70: 3159-3169
52. De Villiers EM: Heterogeneity of the human papillomavirus group. J Virol 1989; 63: 4898-4903
53. Qu W, Jiang G, Cruz Y, et al: PCR detection of human papillomavirus: comparison between MY09/ MY11 and GP5/GP6 primer systems. J Clin Microbiol 1997; 35: 1304-1310
54. Abreu AL, Souza RP, Gimenes F, Consolaro ME: A review of methods for detect human papillomavirus infection. Virol J 2012; 9: 262
55. De Villiers EM: Cross-roads in the classification of papillomaviruses. Virology 2013; 445: 2-10
56. Burk RD, Harari A, Chen Z: Human papillomavirus genome variants. Virology 2013;445:232-243
57. Bernard HU: The clinical importance of the nomenclature, evolution and taxonomy of human papillomaviruses. J Clin Virol 2005; 32(suppl 1):S1-S6
58. Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD: Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol 2005; 79: 7014-7023
59. Gottschling M, Kohler A, Stockfleth E, Nindl I: Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data. Mol Phylogenet Evol 2007; 42: 213-222
60. Egawa K, Delius H, Matsukura T, Kawashima M, de Villiers EM: Two novel types of human papillomavirus, HPV 63 and HPV 65: comparisons of their clinical and histological features and DNA sequences to other HPV types. Virology 1993; 194: 789-799
61. Bottalico D, Chen Z, Dunne A, et al: The oral cavity contains abundant known and novel human papillomaviruses from the Betapapillomavirus and Gammapapillomavirus genera. J Infect Dis 2011; 204: 787-792
62. Gage JC, Schiffman M, Solomon D, et al: Risk of precancer determined by HPV genotype combinations in women with minor cytologic abnormalities. Cancer Epidemiol Biomarkers Prev 2013; 22: 1095-1101
63. Burk RD, Terai M, Gravitt PE, et al: Distribution of human papillomavirus types 16 and 18 variants in squamous cell carcinomas and adenocarcinomas of the cervix. Cancer Res 2003; 63: 7215-7220
64. Li N, Franceschi S, Howell-Jones R, Snijders PJ, Clifford GM: 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
65. Chen Z, Schiffman M, Herrero R, et al: Evolution and Taxonomic Classification of Alphapapillomavirus
66. Complete Genomes: HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70. PloS One 2013;8:e72565
67. Chan SY, Ho L, Ong CK, et al: Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind. J Virol 1992; 66: 2057-2066
68. Smith B, Chen Z, Reimers L, et al: Sequence imputation of HPV16 genomes for genetic association studies. PloS One 2011; 6:e21375
69. Chan SY, Chew SH, Egawa K, et al: Phylogenetic analysis of the human papillomavirus type 2 (HPV-2), HPV-27, and HPV-57 group, which is associated with common warts. Virology 1997; 239: 296-302
70. Yamada T, Manos MM, Peto J, et al: Human papillomavirus type 16 sequence variation in cervical cancers: A worldwide perspective. J Virol 1997; 71: 2463-2472
71. Guan P, Howell-Jones R, Li N, et al: Human papillomavirus types in 115,789 HPV-positive women: A meta-analysis from cervical infection to cancer. Int J Cancer 2012; 131: 2349-2359
72. Castle PE, Porras C, Quint WG, et al: Comparison of two PCR-based human papillomavirus genotyping methods. J Clin Microbiol 2008; 46: 3437-3445
73. Xi LF, Schiffman M, Koutsky LA, et al: Persistence of newly detected human papillomavirus type 31 infection, stratified by variant lineage. Int J Cancer 2013; 132: 549-555
74. Rositch AF, Koshiol J, Hudgens MG, et al: Patterns of persistent genital human papillomavirus infection among women worldwide: A literature review and meta-analysis. Int J Cancer 2013; 133: 1271-1285
75. Xi LF, Schiffman M, Koutsky LA, et al: Association of human papillomavirus type 31 variants with risk of cervical intraepithelial neoplasia grades 2-3. Int J Cancer 2012; 131: 2300-2307
76. Conway C, Chalkley R, High A, et al: Next-generation sequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors. J Mol Diagn 2012; 14: 104-111
77. Foulongne V, Sauvage V, Hebert C, et al: Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PloS One 2012; 7:e38499
78. Johansson H, Bzhalava D, Ekstrom J, Hultin E, Dillner J, Forslund O: Metagenomic sequencing of 'HPV-negative' condylomas detects novel putative HPV types. Virology 2013; 440: 1-7
79. Clarke MA, Wentzensen N, Mirabello L, et al: Human papillomavirus DNA methylation as a potential biomarker for cervical cancer. Cancer Epidemiol Biomarkers Prev 2012; 21: 2125-2137
80. Mirabello L, Schiffman M, Ghosh A, et al: Elevated methylation of HPV16 DNA is associated with the development of high grade cervical intraepithelial neoplasia. Int J Cancer 2013; 132: 1412-1422
81. Mirabello L, Sun C, Ghosh A, et al: Methylation of human papillomavirus type 16 genome and risk of cervical precancer in a Costa Rican population. J Natl Cancer Inst 2012; 104: 556-565
82. Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22: 2688-2690.