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DI-tector: defective interfering viral genomes' detector for next-generation sequencing data
Guillaume Beauclair1,2, Marie Mura1,2,3, Chantal Combredet1,2
1Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France.
RNA (New York, N.Y.)
|July 18, 2018
Summary
DI-tector is a new tool that identifies defective viral genomes (DVGs) in RNA virus replication. This program accurately detects novel copy-back/snap-back DVGs, improving our understanding of viral pathogenesis and innate immunity.
Area of Science:
- Virology
- Genomics
- Immunology
Background:
- Defective interfering (DI) genomes, also known as defective viral genomes (DVGs), are truncated viral genomes produced during the replication of many viruses, including live viral vaccines.
- Copy-back (cb) and snap-back (sb) DI genomes are specific types generated during RNA virus replication, with 5' cb/sb DI genomes possessing immunostimulatory properties crucial for host innate immune system recognition and viral pathogenesis.
Purpose of the Study:
- To develop and validate a user-friendly, freely available program named DI-tector for identifying and characterizing cb/sb DI genomes from next-generation sequencing (NGS) data.
- To assess the capability of DI-tector in revealing the complete landscape of DI genome populations in virus-infected cells.
Main Methods:
- Development of DI-tector, a computational tool for analyzing NGS data to detect cb/sb DI genomes.
- Application of DI-tector to next-generation sequencing data from measles virus (MV)-infected cells.
- Validation of novel DI genome findings using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and reverse transcription polymerase chain reaction (RT-PCR).
- Performance evaluation of DI-tector using diverse experimental and simulated datasets to ascertain its specificity and sensitivity.
Main Results:
- DI-tector successfully confirmed the presence of known 5' cb genomes in MV-infected cells.
- The tool identified a previously unknown 5' cb genome and various 3' cb/sb genomes in MV-infected cells, which were not detectable by conventional methods.
- Experimental validation confirmed the existence of these novel cb/sb genomes, demonstrating DI-tector's efficacy.
- Performance assessments indicated robust specificity and sensitivity of DI-tector across different datasets.
Conclusions:
- DI-tector is a reliable and effective tool for the unbiased detection and characterization of DI viral genomes, including 5' cb/sb DI genomes, within NGS data.
- The program facilitates a comprehensive understanding of the DI genome population during viral infections.
- DI-tector is proposed as a universal tool for researchers studying viral pathogenesis and innate immunity.