SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

Area of Science:

• Clinical diagnostics
• Molecular biology
• Infectious disease research

Background:

• Global SARS-CoV-2 testing demands strained supply chains for reagents and materials.
• Conventional nucleic acid testing for SARS-CoV-2 requires nasopharyngeal swabs, transport media, and nucleic acid extraction.
• Shortages necessitated the development of streamlined laboratory testing protocols.

Purpose of the Study:

• To develop and validate SwabExpress, a simplified end-to-end protocol for SARS-CoV-2 testing.
• To bypass the need for transport media and nucleic acid extraction in COVID-19 testing.
• To address reagent and supply shortages impacting large-scale clinical testing.

Main Methods:

• Evaluated anterior nares swabs transported dry and eluted in low-TE buffer for direct-to-RT-qPCR analysis.
• Validated heat treatment for viral inactivation and incorporated proteinase K digestion to minimize amplification interference.
• Optimized and tested the protocol on archived and prospectively collected swab specimens.

Main Results:

• SwabExpress demonstrated a low limit of detection (2-4 molecules/µL), 100% sensitivity, and 99.4% specificity compared to traditional RT-qPCR.
• The protocol outperformed an automated extraction system on real-world specimens.
• SwabExpress significantly reduced cost and hands-on time for COVID-19 testing.

Conclusions:

• SwabExpress provides a simplified workflow for scaled COVID-19 testing without compromising performance.
• This protocol can serve as a model for simplifying PCR-based clinical laboratory tests, especially during pandemics.
• The method is crucial for maintaining diagnostic capacity amidst critical shortages.