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

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 extractio...

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Bibliographic Details
Published in:Scientific reports 2023-11, Vol.13 (1), p.20349-20349, Article 20349
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
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Language:English
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-023-47190-w