Acknowledgements: We would like to thank Professor Ruijie Deng for providing the pseudovirus. A.P.I. and J.B.E. acknowledge support from BBSRC grant BB/R022429/1, EPSRC grant EP/V049070/1, and Analytical Chemistry Trust Fund grant 600322/05. This project has also received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement Nos. 724300 and 875525). A.E. and P.G. acknowledge support from the Ministry of Education and Science of the Russian Federation, Agreement No. 075-15-2022-264, unique scientific facility reg. No 2512530. R.R. and Y.K. acknowledge support from Japan Society for the Promotion of Science KAKENHI Grants 21H01770, 22K04890, and World Premier International Research Center Initiative (WPI), MEXT, Japan. Research in the P.C. laboratory is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC2058), the UK Medical Research Council (CC2058), and the Wellcome Trust (CC2058). This research was funded in whole, or in part, by the Wellcome Trust (CC2058). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. We acknowledge the UK Health Security Agency and St Mary’s Hospital for providing clinical samples.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
