Quantification of virus-infected cells using RNA FISH-Flow

Cody J Warren; Arturo Barbachano-Guerrero; Devra Huey; Qing Yang; Emma R Worden-Sapper; Jens H Kuhn; Sara L Sawyer

doi:10.1016/j.xpro.2023.102291

Quantification of virus-infected cells using RNA FISH-Flow

STAR Protoc. 2023 May 18;4(2):102291. doi: 10.1016/j.xpro.2023.102291. Online ahead of print.

Authors

Cody J Warren¹, Arturo Barbachano-Guerrero², Devra Huey³, Qing Yang², Emma R Worden-Sapper², Jens H Kuhn⁴, Sara L Sawyer⁵

Affiliations

¹ Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA. Electronic address: warren.802@osu.edu.
² BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA.
³ Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA.
⁴ Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
⁵ BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA. Electronic address: ssawyer@colorado.edu.

Abstract

We present a protocol to detect cells that have been infected by RNA viruses. The method, RNA fluorescence in situ hybridization flow cytometry (RNA FISH-Flow), uses 48 fluorescently labeled DNA probes that hybridize in tandem to viral RNA. RNA FISH-Flow probes can be synthesized to match any RNA virus genome, in either sense or anti-sense, enabling detection of genomes or replication intermediates within cells. Flow cytometry enables high-throughput analysis of infection dynamics within a population at the single cell level. For complete details on the use and execution of this protocol, please refer to Warren et al. (2022).¹.

Keywords: In Situ Hybridization; Microbiology; Molecular Biology.

Abstract

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