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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): 71. doi:10.3390/v12010071.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-F661-8 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-580E-9
Genre: Journal Article

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© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

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 Creators:
Kupke, Sascha Young1, Author              
Ly, Lam-Ha2, Author
Börno, Stefan T. 3, Author
Ruff, Alexander1, Author              
Timmermann, Bernd4, Author
Vingron, Martin2, Author
Haas , Stefan2, Author
Reichl, Udo1, 4, Author              
Affiliations:
1Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, ou_1738140              
2Max Planck Inst Mol Genet, Dept Computat Mol Biol, D-14195 Berlin, Germany, ou_persistent22              
3Max Planck Inst Mol Genet, Sequencing Core Facil, D-14195 Berlin, Germany, ou_persistent22              
4Otto-von-Guericke-Universität Magdeburg, External Organizations, ou_1738156              

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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
 Publication Status: Published in print
 Pages: -
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 Rev. Method: -
 Identifiers: DOI: 10.3390/v12010071
Other: pubdata_escidoc:3216958
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Title: Viruses
Source Genre: Journal
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Publ. Info: Basel : MDPI
Pages: - Volume / Issue: 12 (1) Sequence Number: 71 Start / End Page: - Identifier: ISSN: 1999-4915
CoNE: https://pure.mpg.de/cone/journals/resource/1999-4915