Viral detection and identification in 20 minutes by rapid single-particle fluorescence in-situ hybridization of viral RNA

Abstract

The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 minutes, in both virus cultures and combined throat and nasal swabs without previous purification. This fast and facile workflow is applicable to a wide range of enveloped viruses and can be adapted both as a lab technique and a future diagnostic tool.

High-throughput super-resolution analysis of influenza virus pleomorphism reveals insights into viral spatial organization

“…Electron microscopy images of bacilliforms and short filaments of influenza have suggested that the RNPs that contain the viral RNA cluster at one end of the virus interior, however clear images of the genome have only been obtained in a minority of longer filaments (reviewed in [ 9 ]). In order to clarify the location of RNPs within filaments we used single-molecule fluorescence in situ hybridization (smFISH) to specifically label the influenza NA segment RNA [ 39 ] combined with antibody labelling against the HA protein to outline the filament shape. smFISH uses an array of fluorescently labelled DNA probes that bind to several sites on the viral RNA, thereby accumulating several fluorescent dye molecules on a viral RNA, making it visible as a bright spot.…”