PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

BMC Bioinformatics
Alexis RobitailleMagali Olivier

Abstract

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 N...Continue Reading

References

Jun 12, 2003·Journal of Virological Methods·Ola ForslundGeoff Higgins
Apr 8, 2009·The Lancet Oncology·Véronique BouvardUNKNOWN WHO International Agency for Research on Cancer Monograph Working Group
Mar 9, 2010·Virology·Hans-Ulrich BernardEthel-Michele de Villiers
Feb 3, 2011·Molecular Biology and Evolution·Marc GottschlingIgnacio G Bravo
Jun 4, 2011·Bioinformatics·Simon A Berger, Alexandros Stamatakis
Oct 25, 2012·Nucleic Acids Research·Koenraad Van DoorslaerAlison A McBride
May 21, 2013·Virology·Ethel-Michele de Villiers
Nov 12, 2013·Virology·Johanna EkströmJoakim Dillner
Dec 10, 2013·Seminars in Cancer Biology·Massimo Tommasino
Jan 24, 2014·Japanese Journal of Infectious Diseases·Fumihiko TakeuchiMakoto Kuroda
Apr 1, 2014·Cell·Herbert W Virgin
Nov 13, 2014·International Journal of Cancer. Journal International Du Cancer·L Sara Arroyo MührJoakim Dillner
Jan 13, 2015·Virology·Davit BzhalavaJoakim Dillner
Jan 31, 2015·Evolution, Medicine, and Public Health·Ignacio G Bravo, Marta Félez-Sánchez
May 25, 2015·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·B J KocjanM Poljak
Jan 31, 2017·Nature Reviews. Microbiology·Peter SimmondsF Murilo Zerbini
Aug 26, 2017·Genome Announcements·Rosario N BrancaccioTarik Gheit
Nov 7, 2018·Nature Medicine·Osnat TiroshHeidi H Kong
Aug 21, 2019·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Rossybelle P AmorrortuDana E Rollison

❮ Previous
Next ❯

Citations

Dec 1, 2020·The Journal of Infection·Luisa GalatiTarik Gheit

❮ Previous
Next ❯

Datasets Mentioned

BETA
FJ969907.1

Methods Mentioned

BETA
PCR
amplicon sequencing
PCRs
in silico methods

Software Mentioned

closest
FastQ
TrimGalore
EPA
AlignmentPosition
BlastN
37VIRUSput
RaxML
PaVE
PVAmpliconFinder

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.