An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing

• Published in: Scientific reports Vol. 13; no. 1; pp. 20349 - 12
• Main Authors: Ramos-Mandujano, Gerardo, Grünberg, Raik, Zhang, Yingzi, Bi, Chongwei, Guzmán-Vega, Francisco J., Shuaib, Muhammad, Gorchakov, Rodion V., Xu, Jinna, Tehseen, Muhammad, Takahashi, Masateru, Takahashi, Etsuko, Dada, Ashraf, Ahmad, Adeel Nazir, Hamdan, Samir M., Pain, Arnab, Arold, Stefan T., Li, Mo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.11.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2785; 631/1647; 631/1647/2217; 631/326/2521; 631/326/421; 631/61/514/2254; 692/699/255; 692/699/255/2514; Automation; Clinical Laboratory Techniques - methods; Contamination; Cost-Benefit Analysis; COVID-19; COVID-19 - diagnosis; COVID-19 Testing; Diagnosis; Genomics; Humanities and Social Sciences; Humans; multidisciplinary; Nanoparticles; Nanopore Sequencing; Pandemics; Reagents; Regulatory approval; Reproducibility of Results; RNA, Viral - analysis; RNA, Viral - genetics; SARS-CoV-2 - genetics; Science; Science (multidisciplinary); Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Surveillance
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-47190-w

The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use–with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.