An alternative method for SARS-CoV-2 detection with use modified fluorescent in situ hybridization

Area of Science:

• Molecular Biology
• Virology
• Microbiology

Background:

• Real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) is the standard for SARS-CoV-2 detection but can yield false negatives.
• There is a need for complementary diagnostic tools to enhance SARS-CoV-2 detection accuracy.

Purpose of the Study:

• To develop a highly specific molecular test for detecting and visualizing SARS-CoV-2 infection.
• To evaluate the efficacy of a novel fluorescence in situ hybridization (FISH) method for SARS-CoV-2 diagnosis.

Main Methods:

• A universal probe and specific oligonucleotides with FLAP sequences were designed for FISH-based visualization.
• FISH assay conditions were optimized using SARS-CoV-2 infected Vero CCL-81 cells.
• The FISH method was validated on 290 nasopharyngeal swabs from patients with suspected SARS-CoV-2, comparing results with rRT-PCR.

Main Results:

• The FISH method identified 220 positive and 70 negative results.
• rRT-PCR yielded 200 positive and 90 negative results.
• The differences in detection rates between FISH and rRT-PCR were statistically significant (p=0.008).

Conclusions:

• Fluorescence in situ hybridization (FISH) shows promise as a complementary method for microbiological diagnosis of SARS-CoV-2.
• The developed FISH assay demonstrates high specificity for detecting SARS-CoV-2.
• FISH can aid in improving the accuracy of SARS-CoV-2 diagnostics, potentially reducing false negatives.