Use of a simplified sample processing step without RNA extraction for direct SARS-CoV-2 RT-PCR detection

Area of Science:

• Virology
• Molecular Biology
• Public Health

Background:

• The COVID-19 pandemic led to critical shortages of RNA extraction kits essential for RT-PCR testing.
• Nucleic acid extraction is a standard but resource-intensive step in SARS-CoV-2 detection.

Purpose of the Study:

• To evaluate a simplified heat-RNA release method as an alternative to automated RNA extraction for SARS-CoV-2 detection.
• To assess the diagnostic performance of heat-RNA release compared to a standard extraction method.

Main Methods:

• Nasopharyngeal samples were tested for SARS-CoV-2 using RT-PCR with the ChromaCode HDPCR™ SARS-CoV-2 assay.
• Samples were processed using both a simplified heat-RNA release method and an automated RNA extraction system (EMAG).
• Results from both methods were compared to determine detection concordance.

Main Results:

• The heat-RNA release method correctly identified 94% (81/86) of SARS-CoV-2 positive nasopharyngeal samples.
• The five missed samples had low viral loads (mean Ct value of 35), suggesting minimal impact on high-load cases.
• This method demonstrated comparable detection rates for the majority of positive samples.

Conclusions:

• A simplified heat-RNA release method is a practical and effective alternative for SARS-CoV-2 detection.
• This approach can mitigate supply chain issues and reduce costs associated with RNA extraction reagents.
• The method supports continued COVID-19 surveillance and diagnostics during reagent scarcity.