The 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. We 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. PVAmpliconFinder 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.

中文翻译：

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PVAmpliconFinder：通过高通量扩增子测序鉴定人乳头瘤病毒的工作流程。


通过有针对性的湿实验室方法检测已知的人乳头瘤病毒 (PV) 传统上使用基于 PCR 的方法与桑格测序相结合。随着下一代测序 (NGS) 的引入，可以重新审视这些方法以整合 NGS 的测序能力。尽管已经开发出用于宏基因组方法的计算工具来在NGS数据中搜索已知或新型病毒，但没有合适的工具可用于从基于扩增子的方法产生的数据中分类和识别新型病毒序列。我们开发了 PVAmpliconFinder，这是一种数据分析工作流程，旨在使用简并 PV 引物从 NGS 扩增子测序中快速识别和分类已知的和潜在的新乳头瘤病毒科序列。在这里，我们使用从健康个体的人类皮肤拭子样本和口腔冲洗液的扩增子测序获得的生物数据来描述 PVAmpliconFinder 的功能及其实现。 PVAmpliconFinder 鉴定出了假定的新 HPV 序列，其中包括通过湿实验室实验验证的序列。 PVAmpliconFinder 可以轻松修改并应用于其他病毒家族。 PVAmpliconFinder 通过提供越来越多地用于临床研究的 NGS 扩增子测序分析解决方案来弥补这一空白。 PVAmpliconFinder 工作流程及其源代码可在 GitHub 平台上免费获取：https://github.com/IARCbioinfo/PVAmpliconFinder。