ArticleMed (New York, N.Y.)2021
Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing.
Article in Med (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review on the incidence of influenza viruses in wastewater matrices: Implications for public health.PloS one · 2024Pooled it
- Stable bioreactor control reveals acidic pH-driven metabolic reprogramming and mitochondrial dysfunction in human lymphoblastoid cells.Communications biology · 2026Article
- Wastewater-based surveillance of microbial pathogens in GCC countries (2015-2025): a scoping review and questionnaire survey with stakeholders.Frontiers in public health · 2026Article
- Long-Term Sewage Survey of SARS-CoV-2, Influenza A and Respiratory Syncytial Virus (RSV), and Correlation to Human Cases in a City with One Million Inhabitants.Microorganisms · 2025Article
- RT-RPA as a dual tool for detection and phylogenetic analysis of epidemic arthritogenic alphaviruses.Scientific reports · 2024Article
- An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.Scientific reports · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- The Detection of Periodic Reemergence Events of SARS-CoV-2 Delta Strain in Communities Dominated by Omicron.Pathogens (Basel, Switzerland) · 2022Article
- Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations.International journal of environmental research and public health · 2022Review
- Recent advances in the biosensors application for the detection of bacteria and viruses in wastewater.Journal of environmental chemical engineering · 2022Review
- Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function.International journal of biological macromolecules · 2022Article
- Nanopore sequencing technology and its application in plant virus diagnostics.Frontiers in microbiology · 2022Review
- The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale.Pathogens (Basel, Switzerland) · 2021Article
- Genome Editing Technologies as Cellular Defense Against Viral Pathogens.Frontiers in cell and developmental biology · 2021Review
- The Complexity of Co-Infections in the Era of COVID-19.SN comprehensive clinical medicine · 2021Review
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed 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 nanopore sequencing of isothermal rapid viral amplification for near real-time analysis (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 coronavirus disease 2019 (COVID-19). Additionally, NIRVANA could simultaneously detect SARS-CoV-2 and pepper mild mottle virus (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).
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