Influenza A viruses (IAVs) remain a significant global health burden. Activation of the innate immune response is important for controlling early virus replication and spread. It is unclear how early IAV replication events contribute to immune detection. Additionally, while many cell types in the lung can be infected, it is not known if all cell types contribute equally to establish the antiviral state in the host. Here, we use single-cycle influenza A viruses (scIAVs) to characterize the early immune response to IAV in vitro and in vivo. We found that the magnitude of virus replication contributes to antiviral gene expression within infected cells prior to the induction of a global response. We also developed a scIAV that is only capable of undergoing primary transcription, the earliest stage of virus replication. Using this tool, we uncovered replication stage-specific responses in vitro and in vivo. Using several innate immune receptor knockout cell lines, we identify RIG-I as the predominant antiviral detector of primary virus transcription and amplified replication in vitro. Through a Cre-inducible reporter mouse, we used scIAVs expressing Cre-recombinase to characterize cell type-specific responses in vivo. Individual cell types upregulate unique sets of antiviral genes in response to both primary virus transcription and amplified replication. We also identified antiviral genes that are only upregulated in response to direct infection. Altogether, these data offer insight into the early mechanisms of antiviral gene activation during influenza A infection.
Bibliographical noteFunding Information:
This work was supported by National Institutes of Health (https://www.nih.gov/) R01 AI148669 and R01 AI132962 to RAL. EJF was supported by the National Institutes of Health (https://www.nih.gov/) T32 AI007313. MG and KEN were supported by the National Institutes of Health (https://www.nih.gov/) AI118916, AI145296, and AI145359 awards. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to thank the University of Minnesota Genomics Center, Flow Cytometry Facility, and Supercomputing Institute for support of these studies. We would also like to thank Dr. Lauren Hatfield for help generating A549 KO cells.