Metagenomic sequencing of "HPV-negative" condylomas detects novel putative HPV types

Virology

Volumn 440, Issue 1, 2013, Pages 1-7

  Johansson, Hanna ^a   Bzhalava, Davit ^b   Ekström, Johanna ^a   Hultin, Emilie ^b   Dillner, Joakim ^a,b   Forslund, Ola ^a  

^a LUND UNIVERSITY   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

Condyloma; High throughput sequencing; Human papillomavirus

Indexed keywords

ADULT; ARTICLE; BETAPAPILLOMAVIRUS; BETAPAPILLOMAVIRUS TYPE 105; BETAPAPILLOMAVIRUS TYPE 124; BETAPAPILLOMAVIRUS TYPE 5; CLINICAL ARTICLE; CONDYLOMA; CONTROLLED STUDY; FEMALE; GAMMAPAPILLOMAVIRUS; GAMMAPAPILLOMAVIRUS TYPE 130; GAMMAPAPILLOMAVIRUS TYPE 150; GAMMAPAPILLOMAVIRUS TYPE 50; HUMAN; HUMAN PAPILLOMAVIRUS TYPE 57; HUMAN PAPILLOMAVIRUS TYPE 58; HUMAN PAPILLOMAVIRUS TYPE 6; HUMAN PAPILLOMAVIRUS TYPE 66; MALE; METAGENOMICS; MOLLUSCUM CONTAGIOSUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRUS DETECTION; VIRUS GENOME; WART VIRUS;

ADOLESCENT; ADULT; CONDYLOMATA ACUMINATA; FEMALE; GENOME, VIRAL; HUMANS; MALE; METAGENOMICS; MIDDLE AGED; MOLLUSCUM CONTAGIOSUM; MOLLUSCUM CONTAGIOSUM VIRUS; PAPILLOMAVIRIDAE; YOUNG ADULT;

BETAPAPILLOMAVIRUS; GAMMAPAPILLOMAVIRUS; HUMAN PAPILLOMAVIRUS;

EID: 84876418539     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2013.01.023     Document Type: Article

References (37)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Antonsson A., Erfurt C., Hazard K., Holmgren V., Simon M., Kataoka A., Hossain S., Hakangard C., Hansson B.G. Prevalence and type spectrum of human papillomaviruses in healthy skin samples collected in three continents. J. Gen. Virol. 2003, 84:1881-1886.
3. Antonsson A., Forslund O., Ekberg H., Sterner G., Hansson B.G. The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses. J. Virol. 2000, 74:11636-11641.
4. Antonsson A., Karanfilovska S., Lindqvist P.G., Hansson B.G. General acquisition of human papillomavirus infections of skin occurs in early infancy. J. Clin. Microbiol. 2003, 41:2509-2514.
5. Aubin F., Pretet J.L., Jacquard A.C., Saunier M., Carcopino X., Jaroud F., Pradat P., Soubeyrand B., Leocmach Y., Mougin C., Riethmuller D. Human papillomavirus genotype distribution in external acuminata condylomata: a Large French National Study (EDiTH IV). Clin. Infect. Dis. 2008, 47:610-615.
6. 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.
7. Bottalico D., Chen Z., Dunne A., Ostoloza J., McKinney S., Sun C., Schlecht N.F., Fatahzadeh M., Herrero R., Schiffman M., Burk R.D. The oral cavity contains abundant known and novel human papillomaviruses from the Betapapillomavirus and Gammapapillomavirus genera. J. Infect. Dis. 2011, 204:787-792.
8. Castronovo C., Lebas E., Nikkels-Tassoudji N., Nikkels A.F. Viral infections of the pubis. Int. J. STD AIDS 2012, 23:48-50.
9. Chen Z., Schiffman M., Herrero R., Desalle R., Burk R.D. Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. Virology 2007, 360:447-453.
10. Chouhy D., Gorosito M., Sanchez A., Serra E.C., Bergero A., Fernandez Bussy R., Giri A.A. 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 2010, 397:205-216.
11. de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U., zur Hausen H. Classification of papillomaviruses. Virology 2004, 324:17-27.
12. de Villiers E.M., Gunst K. Characterization of seven novel human papillomavirus types isolated from cutaneous tissue, but also present in mucosal lesions. J. Gen. Virol. 2009, 90:1999-2004.
13. Didelot X., Bowden R., Wilson D.J., Peto T.E., Crook D.W. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 2012, 13:601-612.
14. Ekstrom J., Bzhalava D., Svenback D., Forslund O., Dillner J. High throughput sequencing reveals diversity of human papillomaviruses in cutaneous lesions. Int. J. Cancer 2011, 129:2643-2650.
15. Ekstrom J., Forslund O., Dillner J. Three novel papillomaviruses (HPV109, HPV112 and HPV114) and their presence in cutaneous and mucosal samples. Virology 2010, 397:331-336.
16. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998, 8:186-194.
17. Favre M., Obalek S., Jablonska S., Orth G. Human papillomavirus (HPV) type 50, a type associated with epidermodysplasia verruciformis (EV) and only weakly related to other EV-specific HPVs. J. Virol. 1989, 63:4910.
18. Forslund O. Genetic diversity of cutaneous human papillomaviruses. J. Gen. Virol. 2007, 88:2662-2669.
19. Forslund O., Lindelof B., Hradil E., Nordin P., Stenquist B., Kirnbauer R., Slupetzky K., Dillner J. High prevalence of cutaneous human papillomavirus DNA on the top of skin tumors but not in "Stripped" biopsies from the same tumors. J. Invest. Dermatol. 2004, 123:388-394.
20. Foulongne V., Sauvage V., Hebert C., Dereure O., Cheval J., Gouilh M.A., Pariente K., Segondy M., Burguiere A., Manuguerra J.C., Caro V., Eloit M. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One 2012, 7:e38499.
21. Gissmann L., deVilliers E.M., zur Hausen H. Analysis of human genital warts (condylomata acuminata) and other genital tumors for human papillomavirus type 6 DNA. Int. J. Cancer 1982, 29:143-146.
22. Human Microbiome Project C. A framework for human microbiome research. Nature 2012, 486:215-221.
23. IARC Human papillomaviruses. IARC Monogr. Eval. Carcinog. Risks Hum. 2012, 100B:255-313.
24. Kocjan B.J., Poljak M., Seme K., Potocnik M., Fujs K., Babic D.Z. Distribution of human papillomavirus genotypes in plucked eyebrow hairs from Slovenian males with genital warts. Infect. Genet. Evol. J. 2005, 5:255-259.
25. Kohler A., Gottschling M., Manning K., Lehmann M.D., Schulz E., Kruger-Corcoran D., Stockfleth E., Nindl I. Genomic characterization of ten novel cutaneous human papillomaviruses from keratotic lesions of immunosuppressed patients. J. Gen. Virol. 2011, 92:1585-1594.
26. Kovanda A., Kocjan B.J., Luzar B., Bravo I.G., Poljak M. Characterization of novel cutaneous human papillomavirus genotypes HPV-150 and HPV-151. PLoS One 2011, 6:e22529.
27. Lasken R.S., Stockwell T.B. Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnol. 2007, 7:19.
28. Li J., Cai H., Xu Z., Wang Q., Hang D., Shen N., Liu M., Zhang C., Abliz A., Ke Y. Nine complete genome sequences of cutaneous human papillomavirus genotypes isolated from healthy skin of individuals living in rural he nan province, china. J. Virol. 2012, 86:11936.
29. Luo C., Tsementzi D., Kyrpides N., Read T., Konstantinidis K.T. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012, 7:e30087.
30. Miller J.R., Delcher A.L., Koren S., Venter E., Walenz B.P., Brownley A., Johnson J., Li K., Mobarry C., Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24:2818-2824.
31. Mokili J.L., Rohwer F., Dutilh B.E. Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2012, 2:63-77.
32. Soderlund-Strand A., Carlson J., Dillner J. Modified general primer PCR system for sensitive detection of multiple types of oncogenic human papillomavirus. J. Clin. Microbiol. 2009, 47:541-546.
33. Sturegård E., Johansson H., Ekström J., Hansson B.-G., Johnsson A., Gustafsson E., Dillner J., Forslund O. Human papillomavirus typing in reporting of condyloma. Sex. Trans. Dis. 2013, 40:123-129.
34. Walboomers J.M., Jacobs M.V., Manos M.M., Bosch F.X., Kummer J.A., Shah K.V., Snijders P.J., Peto J., Meijer C.J., Munoz N. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J. Pathol. 1999, 189:12-19.
35. Walboomers J.M., Meijer C.J. Do HPV-negative cervical carcinomas exist?. J. Pathol. 1997, 181:253-254.
36. Willner D., Haynes M.R., Furlan M., Hanson N., Kirby B., Lim Y.W., Rainey P.B., Schmieder R., Youle M., Conrad D., Rohwer F. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am. J. Respir. Cell Mol. Biol. 2012, 46:127-131.
37. Zachow K.R., Ostrow R.S., Faras A.J. Nucleotide sequence and genome organization of human papillomavirus type 5. Virology 1987, 158:251-254.