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

Enrico Lavezzo, Giulia Masi, Stefano Toppo, Elisa Franchin, Valentina Gazzola, Alessandro Sinigaglia, Serena Masiero, Marta Trevisan, Silvana Pagni, Giorgio Palù, Luisa Barzon

Journal: Viruses 2016;8(3):79

PMID: 26985902

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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.

Address: Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Veneto Institute of Oncology IOV IRCCS, via Gattamelata 64, 35128 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].; Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy. [email protected].

DOI: 10.3390/v8030079

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MeSH Terms: Genetic Variation, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Humans, Multiplex Polymerase Chain Reaction, Oncogene Proteins, Viral, Papillomaviridae, Papillomavirus Infections