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  Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication

Kupke, S. Y., Ly, L.-H., Börno, S. T., Ruff, A., Timmermann, B., Vingron, M., et al. (2020). Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication. Viruses, 12(1): pii: E71. doi:10.3390/v12010071.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-B040-B Version Permalink: http://hdl.handle.net/21.11116/0000-0005-B041-A
Genre: Journal Article

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 Creators:
Kupke, Sascha Young , Author
Ly, Lam-Ha1, Author              
Börno, Stefan T.2, Author              
Ruff, Alexander , Author
Timmermann, Bernd2, Author              
Vingron, Martin1, Author              
Haas, Stefan3, Author              
Affiliations:
1Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
2Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
3Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

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Free keywords: single-cell analysis; influenza A virus; cell-to-cell heterogeneity; defective interfering particles; single-cell RNA sequencing; next-generation sequencing
 Abstract: Virus replication displays a large cell-to-cell heterogeneity; yet, not all sources of this variability are known. Here, we study the effect of defective interfering (DI) particle (DIP) co-infection on cell-to-cell variability in influenza A virus (IAV) replication. DIPs contain a large internal deletion in one of their eight viral RNAs (vRNA) and are, thus, defective in virus replication. Moreover, they interfere with virus replication. Using single-cell isolation and reverse transcription polymerase chain reaction, we uncovered a large between-cell heterogeneity in the DI vRNA content of infected cells, which was confirmed for DI mRNAs by single-cell RNA sequencing. A high load of intracellular DI vRNAs and DI mRNAs was found in low-productive cells, indicating their contribution to the large cell-to-cell variability in virus release. Furthermore, we show that the magnitude of host cell mRNA expression (some factors may inhibit virus replication), but not the ribosome content, may further affect the strength of single-cell virus replication. Finally, we show that the load of viral mRNAs (facilitating viral protein production) and the DI mRNA content are, independently from one another, connected with single-cell virus production. Together, these insights advance single-cell virology research toward the elucidation of the complex multi-parametric origin of the large cell-to-cell heterogeneity in virus infections.

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Language(s): eng - English
 Dates: 2020-01-032020-01-07
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.3390/v12010071
 Degree: -

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Title: Viruses
Source Genre: Journal
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Publ. Info: Basel : MDPI
Pages: - Volume / Issue: 12 (1) Sequence Number: pii: E71 Start / End Page: - Identifier: ISSN: 1999-4915
CoNE: https://pure.mpg.de/cone/journals/resource/1999-4915