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

Gerardo Ramos-Mandujano, Raik Grünberg, Yingzi Zhang, Chongwei Bi, Francisco J. Guzmán-Vega, Muhammad Shuaib, Rodion V. Gorchakov, Jinna Xu, Muhammad Tehseen, Masateru Takahashi, Etsuko Takahashi, Ashraf Dada, Adeel Nazir Ahmad, Samir M. Hamdan, Arnab Pain, Stefan T. Arold*, Mo Li*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number20349
JournalScientific Reports
Volume13
Issue number1
DOIs
StatePublished - Dec 2023

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

  • General

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