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

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

doi:10.1038/s41598-021-98972-z

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

Sci Rep. 2021 Oct 1;11(1):19579. doi: 10.1038/s41598-021-98972-z.

Authors

Christof Hepp¹, Nicolas Shiaelis², Nicole C Robb^{2

3}, Alison Vaughan⁴, Philippa C Matthews⁴, Nicole Stoesser^{4

5}, Derrick Crook^{4

6

5}, Achillefs N Kapanidis⁷

Affiliations

¹ Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK. christof.hepp@physics.ox.ac.uk.
² Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
³ Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
⁴ Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK.
⁵ NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK.
⁶ NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
⁷ Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK. kapanidis@physics.ox.ac.uk.

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 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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

In Situ Hybridization, Fluorescence / methods*
RNA, Viral / isolation & purification*
Viruses / genetics
Viruses / isolation & purification*

Substances

RNA, Viral

Abstract

Publication types

MeSH terms

Substances

Grants and funding