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

作     者：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 

作者机构：Stem Cell and Regeneration Laboratory Bioscience Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Structural Biology and Engineering Computational Biology Research Center. Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Pathogen Genomics Laboratory Bioscience Program Biological and Environmental Science and Engineering (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Health Safety and Environment Department King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Laboratory of DNA Replication and Recombination Bioscience Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Department of Pathology and Laboratory Medicine King Faisal Specialist Hospital and Research Center Jeddah Saudi Arabia College of Medicine Al Faisal University Riyadh Saudi Arabia KAUST Health King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Bioengineering Program Biological and Environmental Science and Engineering Division (BESE) King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia 

出 版 物：《Scientific Reports》 (Sci. Rep.)

年 卷 期：2023年第13卷第1期

页      面：1-12页

基　　金：NTGC OSR, (BAS/1/1020-01-01) Office of Sponsored Research King Abdullah University of Science and Technology, KAUST, (BAS/1/1080-01, URF/1/1976-36) King Abdullah University of Science and Technology, KAUST 

摘      要：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. © 2023, The Author(s).