sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Gioacchino, Andrea Di; Legendre, Rachel; Rahou, Yannis; Najburg, Valérie; Charneau, Pierre; Greenbaum, Benjamin; Tangy, Frédéric; Werf, Sylvie van der; Komarova, Anastassia V.

doi:10.1261/rna.078969.121

Cited by 7 publications

(8 citation statements)

References 27 publications

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“…In addition, the result of the program must be contextualized depending on the type of virus. In some RNA viruses, such as for SARS-CoV-2, translation of their structural proteins is performed from subgenomic fragments (sgRNA) [ 35 , 40 , 41 , 42 , 43 ]. These fragments will be identified as deletions by the program so if they are not of interest to the user, they should be filtered out of the output.…”

Section: Methodsmentioning

confidence: 99%

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data

Olmo-Uceda

Muñoz-Sánchez

Lasso-Giraldo

et al. 2022

Viruses

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The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.

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Section: Methodsmentioning

confidence: 99%

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data

Olmo-Uceda

Muñoz-Sánchez

Lasso-Giraldo

et al. 2022

Viruses

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“…Deletions are the most common type of DVGs among RNA viruses (Di Gioacchino et al 2022; Aguilar Rangel et al 2023). They are thought to form through homologous recombination due to observed homology in specific regions and RNA structures (Jennings et al 1983; Saira et al 2013; Poirier et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Accumulation dynamics of defective genomes during experimental evolution of two betacoronaviruses

Hillung,

Olmo-Uceda,

Muñoz-Sánchez

et al. 2024

Preprint

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Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When coinfected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.

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“…Deletions are the most common type of DVGs among RNA viruses [ 13 , 14 ]. They are thought to form through homologous recombination due to observed homology in specific regions and RNA structures [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses

Hillung,

Olmo-Uceda,

Muñoz-Sánchez

et al. 2024

Viruses

View full text Add to dashboard Cite

Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When co-infected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can in some cases disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were the most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though they were less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at a high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.

show abstract

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Cited by 7 publications

References 27 publications

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data

DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data

Accumulation dynamics of defective genomes during experimental evolution of two betacoronaviruses

Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses

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