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Simultaneous identification of viruses and viral variants with programmable DNA nanobait.

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Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.



Prevention, Pneumonia & Influenza, Biodefense, Emerging Infectious Diseases, Genetics, Vaccine Related, Infectious Diseases, Lung, 4.1 Discovery and preclinical testing of markers and technologies, 4 Detection, screening and diagnosis, Infection, 3 Good Health and Well Being

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Nat Nanotechnol

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Springer Science and Business Media LLC
European Commission Horizon 2020 (H2020) ERC (899538)
European Research Council (647144)
European Commission Horizon 2020 (H2020) Marie Sk?odowska-Curie actions (892333)
Wellcome Trust (215515/Z/19/Z)
Biotechnology and Biological Sciences Research Council (BB/I006303/1)
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