Virus Infection Variability by Single-Cell Profiling

• Published in: Viruses Vol. 13; no. 8; p. 1568
• Main Authors: Suomalainen, Maarit, Greber, Urs F
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 09.08.2021; MDPI
• Subjects: Adenoviruses; Animals; cell state; cell-to-cell variability; Chromatin; Click Chemistry - methods; Dengue fever; Flow cytometry; Fluorescence in situ hybridization; Gene expression; Genome, Viral; Genomes; Herpes simplex; Humans; Hybridization; Immune response; Immunity, Innate; Immunofluorescence; In Situ Hybridization, Fluorescence - methods; Infections; Influenza; Innate immunity; Interferon; Localization; Mice; Microscopy; non-genetic variability; Plaques; Proteins; Review; RNAseq; Single-Cell Analysis; single-cell infection; Transcription; Virion - genetics; Virion - metabolism; Virions; Virus Diseases - metabolism; Virus Diseases - virology; virus imaging; Virus Physiological Phenomena; Virus Replication; Viruses; Viruses - classification; Viruses - genetics; Viruses - metabolism; replication; single transcript fluorescence in situ hybridization; transcription; non-genetic variability; click chemistry; RNAseq; egress; single-cell infection; virus imaging; assembly; virus entry; cell-to-cell variability; cell state; persistence and lysis
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v13081568

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.