Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH

Area of Science:

• Virology and Molecular Biology
• Infectious Diseases
• Biotechnology

Background:

• The COVID-19 pandemic is caused by SARS-CoV-2, a positive-sense single-stranded RNA virus.
• Visualizing viral RNA (vRNA) is crucial for studying SARS-CoV-2 replication, developing therapeutics, and understanding infection dynamics.
• Existing methods for vRNA visualization have limitations in sensitivity or application.

Purpose of the Study:

• To design, validate, and apply novel FISH probes (CoronaFISH) for direct visualization of SARS-CoV-2 vRNA.
• To enable sensitive detection of both positive and negative-stranded vRNA in various biological contexts.
• To provide a comprehensive toolkit, including sequences and protocols, for researchers.

Main Methods:

• Design and synthesis of specific FISH probes targeting SARS-CoV-2 RNA.
• Validation of CoronaFISH in African green monkey and human cell lines.
• Application of CoronaFISH to patient samples and human tissues, including adaptation for electron microscopy.

Main Results:

• Demonstrated sensitive visualization of SARS-CoV-2 vRNA in diverse cell lines, patient samples, and human tissues.
• Successfully adapted CoronaFISH probes for correlative light and electron microscopy.
• Provided all necessary oligonucleotide sequences, design source code, and a detailed protocol for public use.

Conclusions:

• CoronaFISH offers a sensitive and versatile tool for visualizing SARS-CoV-2 RNA.
• This method will significantly aid research into SARS-CoV-2 biology, COVID-19 pathophysiology, and drug discovery.
• CoronaFISH complements existing techniques and has potential applications in diagnostics.