Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

Elena Rensen; Stefano Pietropaoli; Florian Mueller; Christian Weber; Sylvie Souquere; Sina Sommer; Pierre Isnard; Marion Rabant; Jean-Baptiste Gibier; Fabiola Terzi; Etienne Simon-Loriere; Marie-Anne Rameix-Welti; Gérard Pierron; Giovanna Barba-Spaeth; Christophe Zimmer

doi:10.26508/lsa.202101124

Journal articles

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

Elena Rensen ^{1, 2} Stefano Pietropaoli ^{1, 2} Florian Mueller ^{1, 2, *} Christian Weber ^{1, 2} Sylvie Souquere ³ Sina Sommer ^{1, 2} Pierre Isnard ^{4, 5} Marion Rabant ^{5, 4} Jean-Baptiste Gibier ⁶ Fabiola Terzi ⁴ Etienne Simon-Loriere ^{7, 2} Marie-Anne Rameix-Welti ^{8, 9} Gérard Pierron ^{10, *} Giovanna Barba-Spaeth ^{11, *} Christophe Zimmer ^{2, 1, *}

* Corresponding author

1 Imagerie et Modélisation - Imaging and Modeling

2 UP - Université de Paris

3 AMMICa - Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse

4 Département Croissance et Signalisation [Paris]

INEM - UM 111 (UMR 8253 / U1151) - Institut Necker Enfants-Malades

5 CHU Necker - Enfants Malades [AP-HP]

6 CHU Lille

7 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses

8 2I - Infection et inflammation

9 Hôpital Ambroise Paré [AP-HP]

10 IGR - Institut Gustave Roussy

11 Virologie Structurale - Structural Virology

Abstract : The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize vRNA directly in infected cells are critical to analyze the viral replication cycle, screen for therapeutic molecules, or study infections in human tissue. Here, we report the design, validation, and initial application of FISH probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy. We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening, and diagnostics.

Document type :

Journal articles

Domain :

Life Sciences [q-bio]

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https://hal-pasteur.archives-ouvertes.fr/pasteur-03518024
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Submitted on : Saturday, January 8, 2022 - 6:56:11 PM
Last modification on : Wednesday, January 19, 2022 - 1:20:02 PM

Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

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Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

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