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    Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing.

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    Type
    Article
    Authors
    Bi, Chongwei
    Ramos Mandujano, Gerardo
    Tian, Yeteng
    Hala, Sharif cc
    Xu, Jinna
    Mfarrej, Sara
    Esteban, Concepcion Rodriguez
    Delicado, Estrella Nuñez
    Alofi, Fadwa S
    Khogeer, Asim
    Hashem, Anwar M
    Almontashiri, Naif A M
    Pain, Arnab cc
    Izpisua Belmonte, Juan Carlos
    Li, Mo cc
    KAUST Department
    Bioscience Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
    Date
    2021-04-06
    Embargo End Date
    2023-04-06
    Submitted Date
    2020-12-09
    Permanent link to this record
    http://hdl.handle.net/10754/668596
    
    Metadata
    Show full item record
    Abstract
    BackgroundStrategies for monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for combating the pandemic. Detection and mutation surveillance of SARS-CoV-2 and other respiratory viruses require separate and complex workflows that rely on highly-specialized facilities, personnel, and reagents. To date, no method can rapidly diagnose multiple viral infections and determine variants in a high-throughput manner.MethodsWe describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes, termed NIRVANA. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus, and monitor mutations for up to 96 samples in real-time.FindingsNIRVANA showed high sensitivity and specificity for SARS-CoV-2 in 70 clinical samples with a detection limit of 20 viral RNA copies per μl of extracted nucleic acid. It also detected the influenza A co-infection in two samples. The variant analysis results of SARS-CoV-2 positive samples mirror the epidemiology of COVID-19. Additionally, NIRVANA could simultaneously detect SARS-CoV-2 and PMMoV (an omnipresent virus and water quality indicator) in municipal wastewater samples.ConclusionsNIRVANA provides high-confidence detection of both SARS-CoV-2 and other respiratory viruses and mutation surveillance of SARS-CoV-2 on the fly. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses.FundingM.L. is supported by KAUST Office of Sponsored Research (BAS/1/1080-01). This work is supported by KAUST Competitive Research Grant (URF/1/3412-01-01, M.L. and J.C.I.B.) and Universidad Catolica San Antonio de Murcia (J.C.I.B.). A.M.H. is supported by Saudi Ministry of Education (project 436).
    Citation
    Bi, C., Ramos-Mandujano, G., Tian, Y., Hala, S., Xu, J., Mfarrej, S., … Li, M. (2021). Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing. Med. doi:10.1016/j.medj.2021.03.015
    Publisher
    Elsevier BV
    Journal
    Med (New York, N.Y.)
    DOI
    10.1016/j.medj.2021.03.015
    PubMed ID
    33821249
    Additional Links
    https://linkinghub.elsevier.com/retrieve/pii/S2666634021001173
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.medj.2021.03.015
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program

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