Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing.
Type
ArticleAuthors
Bi, ChongweiRamos Mandujano, Gerardo
Tian, Yeteng
Hala, Sharif

Xu, Jinna
Mfarrej, Sara
Esteban, Concepcion Rodriguez
Delicado, Estrella Nuñez
Alofi, Fadwa S
Khogeer, Asim
Hashem, Anwar M
Almontashiri, Naif A M
Pain, Arnab

Izpisua Belmonte, Juan Carlos
Li, Mo

KAUST Department
Bioscience ProgramBiological 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
2021-04-06Embargo End Date
2023-04-06Submitted Date
2020-12-09Permanent link to this record
http://hdl.handle.net/10754/668596
Metadata
Show full item recordAbstract
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.2021.03.015Publisher
Elsevier BVJournal
Med (New York, N.Y.)PubMed ID
33821249Additional Links
https://linkinghub.elsevier.com/retrieve/pii/S2666634021001173ae974a485f413a2113503eed53cd6c53
10.1016/j.medj.2021.03.015
Scopus Count
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