Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
Dec 2021
Dec 2021
Historique:
received:
21
05
2021
accepted:
17
08
2021
pubmed:
8
10
2021
medline:
18
1
2022
entrez:
7
10
2021
Statut:
ppublish
Résumé
Simple and standardized approaches for genome analysis of human papillomavirus (HPV) by next-generation sequencing are needed. The aim of the study was to develop a protocol for direct deep sequencing of high-risk (hr) HPV strains, based on the widely used commercial Hybrid Capture 2 (QIAGEN) test, without any additional probe design. This protocol was applied to 15 HPV-positive and two HPV-negative cervical samples or cell lines and validated at the genotype level by comparing the sequencing results to those obtained using a commercial genotyping kit. The performance of our protocol, presented in this proof-of-principle study, supports its use for accurate characterization of genetic variants of hrHPV.
Identifiants
pubmed: 34618227
doi: 10.1007/s00705-021-05259-9
pii: 10.1007/s00705-021-05259-9
doi:
Substances chimiques
DNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
3421-3425Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
Références
de Martel C, Plummer M, Vignat J, Franceschi S (2017) Worldwide burden of cancer attributable to HPV by site, country and HPV type. Int J Cancer 141:664–670. https://doi.org/10.1002/ijc.30716
doi: 10.1002/ijc.30716
pubmed: 28369882
pmcid: 28369882
Walboomers JM, Jacobs MV, Manos MM et al (1999) Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol 189:12–19. https://doi.org/10.1002/(SICI)1096-9896(199909)189:1%3c12::AID-PATH431%3e3.0.CO;2-F
doi: 10.1002/(SICI)1096-9896(199909)189:1<12::AID-PATH431>3.0.CO;2-F
pubmed: 10451482
pmcid: 10451482
Bzhalava D, Eklund C, Dillner J (2015) International standardization and classification of human papillomavirus types. Virology 476:341–344. https://doi.org/10.1016/j.virol.2014.12.028
doi: 10.1016/j.virol.2014.12.028
pubmed: 25577151
Guan P, Howell-Jones R, Li N et al (2012) Human papillomavirus types in 115,789 HPV-positive women: a meta-analysis from cervical infection to cancer. Int J Cancer 131:2349–2359. https://doi.org/10.1002/ijc.27485
doi: 10.1002/ijc.27485
Burk RD, Harari A, Chen Z (2013) Human papillomavirus genome variants. Virology 445:232–243. https://doi.org/10.1016/j.virol.2013.07.018
doi: 10.1016/j.virol.2013.07.018
pubmed: 23998342
Mirabello L, Clarke MA, Nelson CW et al (2018) The intersection of HPV epidemiology, genomics and mechanistic studies of HPV-mediated carcinogenesis. Viruses. https://doi.org/10.3390/v10020080
doi: 10.3390/v10020080
pubmed: 29438321
pmcid: 5850387
Meijer CJLM, Berkhof J, Castle PE et al (2009) Guidelines for human papillomavirus DNA test requirements for primary cervical cancer screening in women 30 years and older. Int J Cancer 124:516–520. https://doi.org/10.1002/ijc.24010
doi: 10.1002/ijc.24010
pubmed: 18973271
pmcid: 2789446
Paget-Bailly P, Meznad K, Bruyère D et al (2019) Comparative RNA sequencing reveals that HPV16 E6 abrogates the effect of E6*I on ROS metabolism. Sci Rep 9:5938. https://doi.org/10.1038/s41598-019-42393-6
doi: 10.1038/s41598-019-42393-6
pubmed: 30976051
pmcid: 6459911
Vaisman CE, Del Moral-Hernandez O, Moreno-Campuzano S et al (2018) C33-A cells transfected with E6*I or E6*II the short forms of HPV-16 E6, displayed opposite effects on cisplatin-induced apoptosis. Virus Res 247:94–101. https://doi.org/10.1016/j.virusres.2018.02.009
doi: 10.1016/j.virusres.2018.02.009
pubmed: 29452161
Jacquin E, Saunier M, Mauny F et al (2013) Real-time duplex PCR for simultaneous HPV 16 and HPV 18 DNA quantitation. J Virol Methods 193:498–502. https://doi.org/10.1016/j.jviromet.2013.07.023
doi: 10.1016/j.jviromet.2013.07.023
pubmed: 23891872
Zehbe I, Voglino G, Delius H et al (1998) Risk of cervical cancer and geographical variations of human papillomavirus 16 E6 polymorphisms. Lancet 352:1441–1442. https://doi.org/10.1016/S0140-6736(05)61263-9
doi: 10.1016/S0140-6736(05)61263-9
pubmed: 9807995
de Villiers E-M (2013) Cross-roads in the classification of papillomaviruses. Virology 445:2–10. https://doi.org/10.1016/j.virol.2013.04.023
doi: 10.1016/j.virol.2013.04.023
pubmed: 23683837
Barzon L, Militello V, Pagni S, Palù G (2012) Comparison of INNO-LiPA Genotyping Extra and Hybrid Capture 2 assays for detection of carcinogenic human papillomavirus genotypes. J Clin Virol 55:256–261. https://doi.org/10.1016/j.jcv.2012.07.013
doi: 10.1016/j.jcv.2012.07.013
pubmed: 22877561
Poljak M, Marin IJ, Seme K, Vince A (2002) Hybrid Capture II HPV Test detects at least 15 human papillomavirus genotypes not included in its current high-risk probe cocktail. J Clin Virol 25:89–97. https://doi.org/10.1016/S1386-6532(02)00187-7
doi: 10.1016/S1386-6532(02)00187-7
Tuna M, Amos CI (2017) Next generation sequencing and its applications in HPV-associated cancers. Oncotarget 8:8877–8889. https://doi.org/10.18632/oncotarget.12830
doi: 10.18632/oncotarget.12830
pubmed: 27784002
Zhu B, Xiao Y, Yeager M et al (2020) Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance. Nat Commun 11:886. https://doi.org/10.1038/s41467-020-14730-1
doi: 10.1038/s41467-020-14730-1
pubmed: 32060290
pmcid: 7021686
Mirabello L, Yeager M, Cullen M et al (2016) HPV16 sublineage associations with histology-specific cancer risk using HPV whole-genome sequences in 3200 women. J Natl Cancer Inst. https://doi.org/10.1093/jnci/djw100
doi: 10.1093/jnci/djw100
pubmed: 27130930
pmcid: 5939630
Mirabello L, Yeager M, Yu K et al (2017) HPV16 E7 genetic conservation is critical to carcinogenesis. Cell 170:1164-1174.e6. https://doi.org/10.1016/j.cell.2017.08.001
doi: 10.1016/j.cell.2017.08.001
pubmed: 28886384
pmcid: 5674785