A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples
AuthorsMandujano, Gerardo Ramos-
Salunke, Rahul Pandurang
Rachmadi, Andri Taruna
Alofi, Fadwa S.
Hashem, Anwar M.
Almontashiri, Naif A. M.
KAUST DepartmentAdvanced Membranes and Porous Materials Research Center
Biological and Environmental Science and Engineering (BESE) Division
Environmental Microbial Safety and Biotechnology Lab
Environmental Science and Engineering Program
Laboratory of DNA Replication and Recombination
Pathogen Genomics Laboratory
Physical Science and Engineering (PSE) Division
Water Desalination and Reuse Research Center (WDRC)
KAUST Grant NumberBAS/1/1080-01
Online Publication Date2021-02-22
Print Publication Date2021-04
Permanent link to this recordhttp://hdl.handle.net/10754/663963
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AbstractMolecular diagnosis and surveillance of pathogens such as SARS-CoV-2 depend on nucleic acid isolation. Pandemics at the scale of COVID-19 can cause a global shortage of proprietary commercial reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. An open-source method, magnetic-nanoparticle-aided viral RNA isolation from contagious samples (MAVRICS), built upon readily available reagents, and easily assembled in any basically equipped laboratory, is thus developed. The performance of MAVRICS is evaluated using validated pathogen detection assays and real-world and contrived samples. Unlike conventional methods, MAVRICS works directly in samples inactivated in phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. MAVRICS allows wastewater biomass immobilized on membranes to be directly inactivated and lysed in TRIzol followed by RNA extraction by magnetic nanoparticles, thereby greatly reducing biohazard risk and simplifying processing procedures. Using 39 COVID-19 patient samples and two wastewater samples, it is shown that MAVRICS rivals commercial kits in detection of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. Therefore, MAVRICS is safe, fast, and scalable. It is field-deployable with minimal equipment requirements and could become an enabling technology for widespread testing and wastewater monitoring of diverse pathogens.
CitationRamos-Mandujano, G., Salunke, R., Mfarrej, S., Rachmadi, A. T., Hala, S., Xu, J., … Li, M. (2021). A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples. Global Challenges, 2000068. doi:10.1002/gch2.202000068
SponsorsThe authors thank KAUST Rapid Research Response Team (R3T) for supporting the research during the COVID-19 crisis. The authors thank members of the KAUST R3T for generously sharing materials and advices. The authors thank Professor Imed Gallouzi of McGill University for the useful discussion. The authors thank members of the Li laboratory, Chongwei Bi, Baolei Yuan, Xuan Zhou, Samhan Alsolami, Yingzi Zhang, and Yeteng Tian for helpful discussions; Marie Krenz Y. Sicat for administrative support. The authors thank members of the labs of Prof. Arnab Pain and Prof. Zhiping Lai for technical assistance. The research of the Li laboratory was supported by KAUST Office of Sponsored Research (OSR), under award numbers BAS/1/1080-01. A.M.H. is supported by funding from the deputyship for Research and Innovation, Ministry of Education in Saudi Arabia (project number 436). N.A.M.A. is supported by funding from the Deanship of Scientific Research, Taibah University, Saudi Arabia (project number AMS-12).
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CollectionsArticles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Advanced Membranes and Porous Materials Research Center; Environmental Science and Engineering Program; Physical Science and Engineering (PSE) Division; Water Desalination and Reuse Research Center (WDRC)
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