Abstract
BackgroundThe detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods.ResultsWe have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. Here, we describe the features of PVAmpliconFinder and its implementation using biological data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals.ConclusionsPVAmpliconFinder identified putative new HPV sequences, including one that was validated by wet-lab experiments. PVAmpliconFinder can be easily modified and applied to other viral families. PVAmpliconFinder addresses a gap by providing a solution for the analysis of NGS amplicon sequencing, increasingly used in clinical research. The PVAmpliconFinder workflow, along with its source code, is freely available on the GitHub platform: https://github.com/IARCbioinfo/PVAmpliconFinder.
Highlights
The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used Polymerase Chain Reaction (PCR)-based methods coupled with Sanger sequencing
We applied the PVAmpliconFinder workflow (Fig. 1) to the data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals, aiming to identify new PVs
Different sets of degenerate primers targeting the L1 region of Human PapillomaVirus (HPV) [7] were used to amplify 47 DNA samples and the amplification products were pooled in 8 DNA sample pools for sequencing
Summary
The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. Computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. PVs are classified into genera, species, and types based on the nucleotide sequence identity of the major capsid protein L1. Human PVs (HPVs) have a tropism for the skin and mucosal epithelia of different anatomical sites and are organized into five major genera: alpha, beta, gamma, mu, and nu [1, 2]. It is important to comprehensively describe the family of HPV types and evaluate their role in human diseases
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call