Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes

Ren Ren, Shenglin Cai (), Xiaona Fang, Xiaoyi Wang, Zheng Zhang, Micol Damiani, Charlotte Hudlerova, Annachiara Rosa, Joshua Hope, Nicola J. Cook, Peter Gorelkin, Alexander Erofeev, Pavel Novak, Anjna Badhan, Michael Crone, Paul Freemont, Graham P. Taylor, Longhua Tang, Christopher Edwards, Andrew Shevchuk, Peter Cherepanov, Zhaofeng Luo, Weihong Tan (), Yuri Korchev, Aleksandar P. Ivanov () and Joshua B. Edel ()
Additional contact information
Ren Ren: Molecular Sciences Research Hub
Shenglin Cai: Molecular Sciences Research Hub
Xiaona Fang: Chinese Academy of Sciences
Xiaoyi Wang: Molecular Sciences Research Hub
Zheng Zhang: Chinese Academy of Sciences
Micol Damiani: Molecular Sciences Research Hub
Charlotte Hudlerova: Molecular Sciences Research Hub
Annachiara Rosa: The Francis Crick Institute
Joshua Hope: The Francis Crick Institute
Nicola J. Cook: The Francis Crick Institute
Peter Gorelkin: National University of Science and Technology “MISIS”
Alexander Erofeev: National University of Science and Technology “MISIS”
Pavel Novak: ICAPPIC Limited
Anjna Badhan: Imperial College London
Michael Crone: Imperial College London
Paul Freemont: Imperial College London
Graham P. Taylor: Imperial College London
Longhua Tang: Zhejiang University
Christopher Edwards: Imperial College London
Andrew Shevchuk: Imperial College London
Peter Cherepanov: The Francis Crick Institute
Zhaofeng Luo: Chinese Academy of Sciences
Weihong Tan: Chinese Academy of Sciences
Yuri Korchev: Imperial College London
Aleksandar P. Ivanov: Molecular Sciences Research Hub
Joshua B. Edel: Molecular Sciences Research Hub

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.

Date: 2023
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DOI: 10.1038/s41467-023-43004-9

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