Résilience - COVID-19 - Résilience - Coronavirus disease 2019

Rapid RNA detection of SARS-CoV-2 and its mutants by ultrabright fluorescent nanoparticles – ViRNASens

Submission summary

The unprecedented spread of COVID-19 requires the development of fast and efficient diagnostic tools in order to stop the chains of contamination and to coordinate the actions at the national and international levels. Particularly, it concerns detection of SARS-CoV-2 and identification of its mutations, which are currently done by enzyme-based RT-PCR (or by a less sensitive antigenic tests) and sequencing, respectively. However, both techniques are relatively slow and expensive, showing their limitations for the massive screening of the population. In this project, we propose a new enzyme-free technique for rapid detection of SARS-CoV-2 and identification of its mutants. It is based on our recent discovery of giant light-harvesting nanoantenna, which can provide direct amplification of fluorescence signal by ~1000-fold. Based on this technique, we have already developed DNA-functionalized nanoparticles that can provide amplified enzyme-free detection of RNA or DNA in solution by simple one-step protocol using total RNA cells extracts or serum medium. As our nanoparticles can convert a single nucleic acid hybridization event into response of thousands of dyes, we can detect clinically relevant RNA biomarkers without enzymatic amplification. Our preliminary results show that these nanoprobes can detect Sindbis virus in the RNA extracts of infected cells and SARS-CoV-2 virus in the samples from patients. We propose to develop a robust technique for detection of SARS-CoV-2 and its mutants in solution and to adapt it to a simple fluorescence plate reader available in most medical laboratories. The project will be composed of three work packages. First, we will establish a standard protocol for of nanoprobes featuring high sensitivity and quantitative ratiometric response to the viral RNA, selectivity to point mutations in RNA and reproducible characteristics. These nanoprobes will be validated for fluorescence detection of synthetic RNA of SARS-CoV-2 and its mutants using a plate reader. Second, we will evaluate our nanoprobes in total RNA lysates of cells infected in vitro with SARS-CoV-2 and its mutants. Third, we will validate detection of SARS-CoV-2 and its mutants in clinical samples. The outcome of this project will be two diagnostics kits for commercialization: (i) basic kit for detection of SARS-CoV-2 in the conserved sequences of the viral genome and (ii) identification of mutants of SARS-CoV-2 using both conserved and variable regions. The consortium is composed of two complementary partners: interdisciplinary chemistry team, which pioneered nanoantenna probes, and a team of molecular virologists specialized in RNA biology. We have a clear commercialization strategy for our technology, which is already protected by three patents. By the end of the project, the developed kits are expected to be commercialized by a local startup, in partnership with a larger biotechnology company. The kits will be proposed to hospitals and medical laboratories as a complementary solution to RT-PCR and gene sequencing, in order to significantly accelerate diagnostics and ensure better prevention of the COVID-19 pandemics.

Project coordination

Andrey KLYMCHENKO (Laboratoire de Bioimagerie et Pathologies (UMR 7021))

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


ARN Architecture et Réactivité de l'ARN (UPR 9002)
LBP Laboratoire de Bioimagerie et Pathologies (UMR 7021)

Help of the ANR 80,000 euros
Beginning and duration of the scientific project: May 2021 - 12 Months

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