Exploring viral infection using single-cell sequencing

•Single-cell sequencing (SCS) is a novel technology that allows analysis of genomic and transcriptomic profiles of individual cells.•Experimental protocols and data analysis are challenging and still under development.•Single-cell sequencing (SCS) brings valuable insight into studying viral infection in relation to host cellular heterogeneity.•The dynamics of viral infection can be explored at single-cell level through sequencing.

Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication.