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

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journal contribution
posted on 2023-11-20, 12:40 authored by 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, Joshua B Edel
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.


Crick (Grant ID: CC2058, Grant title: Cherepanov CC2058)


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