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Viruses 2016, 8(3), 79; doi:10.3390/v8030079

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

1
Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
2
Veneto Institute of Oncology IOV IRCCS, via Gattamelata 64, 35128 Padova, Italy
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Johnson Mak, Peter Walker and Marcus Thomas Gilbert
Received: 24 November 2015 / Revised: 1 March 2016 / Accepted: 7 March 2016 / Published: 14 March 2016
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Abstract

Different human papillomavirus (HPV) types are characterized by differences in tissue tropism and ability to promote cell proliferation and transformation. In addition, clinical and experimental studies have shown that some genetic variants/lineages of high-risk HPV (HR-HPV) types are characterized by increased oncogenic activity and probability to induce cancer. In this study, we designed and validated a new method based on multiplex PCR-deep sequencing of the E6/E7 region of HR-HPV types to characterize HPV intra-type variants in clinical specimens. Validation experiments demonstrated that this method allowed reliable identification of the different lineages of oncogenic HPV types. Advantages of this method over other published methods were represented by its ability to detect variants of all HR-HPV types in a single reaction, to detect variants of HR-HPV types in clinical specimens with multiple infections, and, being based on sequencing of the full E6/E7 region, to detect amino acid changes in these oncogenes potentially associated with increased transforming activity. View Full-Text
Keywords: human papillomavirus; genotyping; next-generation sequencing; E6/E7; subtype; variant; cervical cancer; high-risk HPV; deep sequencing; pyrosequencing human papillomavirus; genotyping; next-generation sequencing; E6/E7; subtype; variant; cervical cancer; high-risk HPV; deep sequencing; pyrosequencing
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Lavezzo, E.; Masi, G.; Toppo, S.; Franchin, E.; Gazzola, V.; Sinigaglia, A.; Masiero, S.; Trevisan, M.; Pagni, S.; Palù, G.; Barzon, L. Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region. Viruses 2016, 8, 79.

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