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

Hepp, Christof; Shiaelis, Nicolas; Robb, Nicole C.; Vaughan, Alison; Matthews, Philippa C.; Stoesser, Nicole; Crook, Derrick; Kapanidis, Achillefs N.

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 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.