Unique Cellular Responses and Novel Long Noncoding RNAs in Respiratory Syncytial Virus/SARS-CoV-2 co-infected lung epithelial cells

This study uses single-cell RNA sequencing (scRNA-seq) to investigate cellular responses to co-infection by HRSV and SARS-CoV-2 in A549-hACE2 cells. Analysis 72 hours post-infection revealed four distinct cell populations: uninfected cells; cells infected with either virus individually; and cells co-infected with both viruses. Among the co-infected cells, two sub-clusters were identified that differed in terms of HRSV replication levels and associated signaling pathways: JAK-STAT in cells with low HRSV replication (cluster 4a) and ERK1/2/MAPK in cells with high HRSV replication (cluster 4b). Co-infection triggered specific patterns of gene expression related to viral defence, innate immunity and type I interferon responses. Notably, 17 long non-coding RNAs (lncRNAs), including some that are not yet annotated, were found to be upregulated, suggesting that they may play a role in the immune response and viral interference. Validation using three independent RNA-seq datasets, including patient samples, confirmed the importance of key markers such as ARHGAP15, ASH1L, MALAT1 and NEAT1 in SARS-CoV-2 infection. These findings highlight the transcriptional signatures of co-infection, identifying potential diagnostic or therapeutic targets and suggesting that viral interactions within single cells may involve competitive or cooperative mechanisms.