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Scientific Fields
Diseases
Organisms
Applications
Technique

Published in RNA (New York, N.Y.) - 16 Jul 2018

Beauclair G, Mura M, Combredet C, Tangy F, Jouvenet N, Komarova AV

Link to Pubmed [PMID] – 30012569

RNA 2018 10;24(10):1285-1296

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 , a user-friendly and freely available program that identifies and characterizes cb/sb genomes from next-generation sequencing (NGS) data. confirmed the presence of 5′ cb genomes in cells infected with measles virus (MV). 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 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 of We propose as a universal tool for the unbiased detection of DI viral genomes, including 5′ cb/sb DI genomes, in NGS data.

https://www.ncbi.nlm.nih.gov/pubmed/30012569