Virus Infection Variability by Single-Cell Profiling

Abstract

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.

Identification of broad anti-coronavirus chemical agents for repurposing against SARS-CoV-2 and variants of concern

“…To address the cell-based anti-viral mechanisms of MB, MPA and POS, we developed a procedure to score intracellular RNA of OC-43 and SARS-CoV-2 at MOI 1 in Huh7 and Huh7-ACE2 cells by fluorescence in situ hybridization using probes against the (+)RNA strand in ORF1a. The procedure was adapted from previous work with adenovirus and rhinovirus ( Yakimovich et al, 2015b ; Suomalainen et al, 2020 ; Suomalainen and Greber, 2021 ). The infection phenotype was scored in MB, MPA, POS and Remdesivir-treated cells by automated measurement of fluorescent puncta representing single RNA molecules.…”

The RGD-binding integrins αvβ6 and αvβ8 are receptors for mouse adenovirus-1 and -3 infection

“…They also stand in contrast to a third class of cell surface molecules, so called facilitators, which assist the function of receptors for the virion. These distinctions are increasingly important, as the cell-to-cell variability of virus infections involves not just the cell internal state [ 59 ], but also the abundance of cell surface molecules and their interactions with virions (for a recent review, see [ 60 ]). To fulfill stringent receptor criteria, we used viral and host genetic engineering, biochemical and cell biological assays as well as molecular modeling, and demonstrate that M1/M3 use RGD-motifs in their FKs to bind with high affinity to αvβ6 and αvβ8 integrins for infection of murine and human cells.…”

Methylene blue, Mycophenolic acid, Posaconazole, and Niclosamide inhibit SARS-CoV-2Omicron variant BA.1 infection of human airway epithelial explant cultures

“…This difference possibly reflects the post-exposure treatment in our case, versus the preexposure treatment by Weiss and colleagues, or alternatively, donor-to-donor variability of the HAEEC. Cell-to-cell and donor-to-donor variability can have a significant influence on the infection outcome both in vivo and in vitro (24)(25)(26). Taken together, Niclo may be considered as a potential inhibitor of SARS-CoV-2 with broad effects on VoC.…”