Rapid, Portable, and Electricity-free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings

• Published in: Analytical chemistry (Washington) Vol. 96; no. 28; pp. 11181 - 11188
• Main Authors: Pennisi, Ivana, Cavuto, Matthew L., Miglietta, Luca, Malpartida-Cardenas, Kenny, Stringer, Oliver W., Mantikas, Katerina-Theresa, Reid, Ruth, Frise, Rebecca, Moser, Nicolas, Randell, Paul, Davies, Frances, Bolt, Frances, Barclay, Wendy, Holmes, Alison, Georgiou, Pantelis, Rodriguez-Manzano, Jesus
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 16-07-2024
• Subjects: Accessibility; Clinical isolates; Construction standards; COVID-19; COVID-19 - diagnosis; COVID-19 - virology; COVID-19 Nucleic Acid Testing - instrumentation; COVID-19 Nucleic Acid Testing - methods; COVID-19 Testing - instrumentation; COVID-19 Testing - methods; Disease control; Electric equipment; Electrical equipment; Electricity; Humans; Molecular Diagnostic Techniques - methods; Nucleic acids; Pandemics; Portability; Reagents; Resource-Limited Settings; RNA, Viral - analysis; RNA, Viral - isolation & purification; Sample preparation; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Severe acute respiratory syndrome coronavirus 2; Specimen Handling - methods; Viral diseases
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/acs.analchem.4c00319

The COVID-19 pandemic has highlighted the need for rapid and reliable diagnostics that are accessible in resource-limited settings. To address this pressing issue, we have developed a rapid, portable, and electricity-free method for extracting nucleic acids from respiratory swabs (i.e. nasal, nasopharyngeal and buccal swabs), successfully demonstrating its effectiveness for the detection of SARS-CoV-2 in residual clinical specimens. Unlike traditional approaches, our solution eliminates the need for micropipettes or electrical equipment, making it user-friendly and requiring little to no training. Our method builds upon the principles of magnetic bead extraction and revolves around a low-cost plastic magnetic lid, called SmartLid, in combination with a simple disposable kit containing all required reagents conveniently prealiquoted. Here, we clinically validated the SmartLid sample preparation method in comparison to the gold standard QIAamp Viral RNA Mini Kit from QIAGEN, using 406 clinical isolates, including 161 SARS-CoV-2 positives, using the SARS-CoV-2 RT-qPCR assays developed by the US Centers for Disease Control and Prevention (CDC). The SmartLid method showed an overall sensitivity of 95.03% (95% CI: 90.44–97.83%) and a specificity of 99.59% (95% CI: 97.76–99.99%), with a positive agreement of 97.79% (95% CI: 95.84–98.98%) when compared to QIAGEN’s column-based extraction method. There are clear benefits to using the SmartLid sample preparation kit: it enables swift extraction of viral nucleic acids, taking less than 5 min, without sacrificing significant accuracy when compared to more expensive and time-consuming alternatives currently available on the market. Moreover, its simplicity makes it particularly well-suited for the point-of-care where rapid results and portability are crucial. By providing an efficient and accessible means of nucleic acid extraction, our approach aims to introduce a step-change in diagnostic capabilities for resource-limited settings.