Single-cell transcriptomic landscape of avian influenza H9N2 virus infection in human and chicken cells.

Avian influenza viruses circulate naturally among migratory wild birds but can occasionally infect other species, including poultry and a broad range of mammals and humans. Although highly pathogenic avian influenza viruses (AIVs) are known to infect humans, low-pathogenic AIVs, particularly H7N9 and H9N2 subtypes, have also caused human infections and pose an ongoing zoonotic risk. In this study, we used single-cell transcriptomics to examine the cellular responses of human (A549) and chicken (DF-1) cells 24 h after infection with the zoonotic H9N2 virus. Our findings revealed distinct transcriptional responses between the two cell lines. Notably, dipeptidyl peptidase-4 (DPP4) and carboxypeptidase Q (CPQ) genes were expressed at significantly higher levels in infected DF-1 cells than in A549 cells, suggesting a potential role in viral replication. Overexpression of CPQ and DPP4 in A549 cells resulted in significantly greater viral replication compared to mock-transfected wild-type cells infected with the avian influenza H9N2 virus. Furthermore, Gene Set Enrichment Analysis of differentially expressed genes revealed downregulation of lipid metabolism pathways in cell clusters highly expressing H9N2 virus genes in both A549 and DF-1 cells, indicating a potential link between host lipid metabolism and H9N2 virus replication. These results provide insights into the transcriptional responses of A549 and DF-1 cells to H9N2 infection and identify candidate host factors and pathways associated with viral replication. These findings provide a foundation for future studies using physiologically relevant models to investigate the cellular determinants of H9N2 infection.