SRA

Influenza defective interfering (DI) viruses have long been considered promising antiviral candidates because of their ability to interfere with replication-competent viruses and to induce antiviral immunity. However, the mechanisms underlying DI-mediated antiviral immunity have not been extensively explored. Here, we demonstrated interferon (IFN) independent protection conferred by influenza DI virus against homologous virus infection in mice deficient in type I and III IFN signaling. By integrating transcriptional and post-transcriptional regulatory data we identified unique host signatures in response to DI co-infection. DI-treated mice exhibited reduced viral transcription, less intense inflammatory and innate immune responses, and primed multiciliated cell differentiation in their lungs at an early stage of infection, even in the absence of type I or III IFNs. This increased multiciliogenesis could also be detected at the protein level by immunofluorescence staining of lung tissue from DI-treated mice. Overall, our study provides mechanistic insight into the protection mediated by DIs, implying a unifying theme involving inflammation and multiciliogenesis in maintaining respiratory homeostasis, and reveals their IFN-independent antiviral activity. Overall design: The firs Dataset consists of a bulk RNA-seq dataset containing 36 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, a miRNA-seq dataset containing 36 libraries generated with QIAseq miRNA library kit, and a viral genome sequencing dataset containing 52 libraries generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera XT DNA library prep kit. This second dataset consists of 31 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module from the first in vivo study presented in the manuscript.