Description: Virus replication displays a large cell-to-cell heterogeneity; yet, not all sources are known. Here, we study the effect of defective interfering (DI) particle (DIP) co-infection on cell-to-cell heterogeneity 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 even interfere with virus replication. Using single-cell isolation and RT-PCR, we uncover a large between-cell variability in the content of DI vRNAs in infected cells, which was confirmed for DI mRNAs by single-cell RNA sequencing. Furthermore, a high load of intracellular DI vRNAs and DI mRNAs was found in low-yield cells , and vice versa, indicating their contribution to the large cell-to-cell heterogeneity in virus release. In addition, we show that the magnitude of host cell mRNA expression (of which 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 the production of viral proteins) and the DI mRNA content are, independently from one another, connected with single-cell virus production. Together, these insights advance single-cell virology research towards elucidation of the complex multi-parametric origin of the large cell-to-cell variability in virus infections.

Data type: raw sequence reads

Sample scope: Multispecies

Relevance: Medical

Last updated: 2019-11-19