DI-tector : defective interfering viral genomes' detector for next-generation sequencing data

RNA
Guillaume BeauclairAnastassia V Komarova

Abstract

Defective interfering (DI) genomes, or defective viral genomes (DVGs), are truncated viral genomes generated during replication of most viruses, including live viral vaccines. Among these, "panhandle" or copy-back (cb) and "hairpin" or snap-back (sb) DI genomes are generated during RNA virus replication. 5' cb/sb DI genomes are highly relevant for viral pathogenesis since they harbor immunostimulatory properties that increase virus recognition by the innate immune system of the host. We have developed DI-tector, a user-friendly and freely available program that identifies and characterizes cb/sb genomes from next-generation sequencing (NGS) data. DI-tector confirmed the presence of 5' cb genomes in cells infected with measles virus (MV). DI-tector also identified a novel 5' cb genome, as well as a variety of 3' cb/sb genomes whose existence had not previously been detected by conventional approaches in MV-infected cells. The presence of these novel cb/sb genomes was confirmed by RT-qPCR and RT-PCR, validating the ability of DI-tector to reveal the landscape of DI genome population in infected cell samples. Performance assessment using different experimental and simulated data sets revealed the robust specificity and sensitivity...Continue Reading

References

Oct 1, 1990·Biologicals : Journal of the International Association of Biological Standardization·C BellocqL Roux
Jan 1, 1973·Annual Review of Microbiology·A S Huang
Jan 1, 1981·Current Topics in Microbiology and Immunology·J Perrault
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Jun 17, 2005·The Journal of General Virology·Daniel KolakofskyRob W H Ruigrok
Apr 25, 2006·Virology·Laura StrahleDaniel Kolakofsky
Oct 20, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Masashi ShingaiTsukasa Seya
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 31, 2009·Reviews in Medical Virology·A C Marriott, N J Dimmock
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Sep 2, 2010·Proceedings of the National Academy of Sciences of the United States of America·Alina BaumAdolfo García-Sastre
Mar 23, 2011·Virulence·Alina Baum, Adolfo García-Sastre
May 12, 2011·PloS One·Dongsheng LiJohn Aaskov
Nov 29, 2011·Briefings in Functional Genomics·Florian MertesAnthony J Brookes
Mar 27, 2012·Briefings in Bioinformatics·Iain MilneDavid Marshall
Apr 19, 2013·RNA Biology·Anastassia V KomarovaFrédéric Tangy
May 17, 2013·Journal of Virology·Kazima SairaUNKNOWN INSIGHT FLU003 Study Group
Oct 9, 2013·Vaccine·Xiomara Mercado-LópezCarolina B López
Dec 20, 2013·Journal of Virology·Collin TimmJohn Yin
Apr 20, 2014·PLoS Pathogens·Simon RungeKarl-Peter Hopfner
May 30, 2014·Journal of Virology·Carolina B López
Mar 25, 2016·ELife·Raul Y Sanchez DavidAnastassia V Komarova

❮ Previous
Next ❯

Citations

May 15, 2019·Annual Review of Virology·Emmanuelle Genoyer, Carolina B López
Jun 5, 2019·Nature Microbiology·Marco Vignuzzi, Carolina B López
Jun 24, 2021·Journal of Virology·Rebecca I JohnsonAnthony Griffiths
Dec 11, 2021·Transboundary and Emerging Diseases·Corey L CampbellRebekah C Kading

❮ Previous
Next ❯

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.