Cell-to-cell variability of
infection has long been known, yet it has remained one of the least understood phenomena in
infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell
RNA sequencing (
scRNA-seq), single-molecule
RNA-fluorescence in situ hybridization (FISH), and
copper(I)-catalyzed
azide-
alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect
infection variability in human and mouse cells. We show how the combined use of
scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how
scRNA-seq profiling and
scRNA-FISH of coxsackie,
influenza,
dengue, zika, and herpes simplex virus
infections uncover transcriptional variability, and how the host
interferon response tunes
influenza and sendai virus
infections. We introduce the concept of "cell state" in
infection variability, and conclude with advances by single-cell simultaneous measurements of
chromatin accessibility and
mRNA counts at high-throughput. Such technology will further dissect the sequence of events in
virus infection and pathology, and better characterize the genetic and
genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.