Single-cell RNA sequencing to understand host-virus interactions

Single-cell RNA sequencing (scRNA-seq) has allowed for the profiling of host and virus transcripts and host-virus interactions at single-cell resolution. This review summarizes the existing scRNA-seq technologies together with their strengths and weaknesses. The applications of scRNA-seq in various virological studies are discussed in depth, which broaden the understanding of the immune atlas, host-virus interactions, and immune repertoire. scRNA-seq can be widely used for virology in the near future to better understand the pathogenic mechanisms and discover more effective therapeutic strategies. •The existing scRNA-seq technologies together with their strengths and weaknesses are summarized.•Applications of scRNA-seq in SARS-CoV-2 and flavivirus studies are extensively discussed.•Applications of scRNA-seq in studying immune atlas, host-virus interactions, and immune repertoire are further explored.