High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore

Kaoru Murakami; Shimpei I. Kubota; Kumiko Tanaka; Hiroki Tanaka; Keiichiroh Akabane; Rigel Suzuki; Yuta Shinohara; Hiroyasu Takei; Shigeru Hashimoto; Yuki Tanaka; Shintaro Hojyo; Osamu Sakamoto; Norihiko Naono; Takayui Takaai; Kazuki Sato; Yuichi Kojima; Toshiyuki Harada; Takeshi Hattori; Satoshi Fuke; Isao Yokota; Satoshi Konno; Takashi Washio; Takasuke Fukuhara; Takanori Teshima; Masateru Taniguchi; Masaaki Murakami

doi:10.1039/D3LC00572K

High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore†

Kaoru Murakami,^ab Shimpei I. Kubota,^ab Kumiko Tanaka,^a Hiroki Tanaka,^a Keiichiroh Akabane,^a Rigel Suzuki,^c Yuta Shinohara,^a Hiroyasu Takei,^d Shigeru Hashimoto,^a Yuki Tanaka,^b Shintaro Hojyo,^ab Osamu Sakamoto,^d Norihiko Naono,^d Takayui Takaai,^e Kazuki Sato,^af Yuichi Kojima,^af Toshiyuki Harada,^h Takeshi Hattori,ⁱ Satoshi Fuke,^k Isao Yokota,^j Satoshi Konno,^f Takashi Washio,^e Takasuke Fukuhara,^c Takanori Teshima,

^gl Masateru Taniguchi

*^e and Masaaki Murakami

*^abm

Author affiliations

* Corresponding authors

^a Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan

^b Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan

^c Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan

^d Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan

^e The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan

^f Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan

^g Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan

^h Department of Respiratory Medicine, Japan Community Healthcare Organization Hokkaido Hospital, Sapporo, Japan

ⁱ Department of Respiratory Medicine, Hokkaido Medical Center, National Hospital Organization, Sapporo, Japan

^j Department of Biostatistics, Faculty of Medicine, Hokkaido University, Sapporo, Japan

^k Department of Respiratory Medicine, KKR Sapporo Medical Center, Sapporo, Japan

^l Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan

^m Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0020, Japan

Abstract

A digital platform that can rapidly and accurately diagnose pathogenic viral variants, including SARS-CoV-2, will minimize pandemics, public anxiety, and economic losses. We recently reported an artificial intelligence (AI)-nanopore platform that enables testing for Wuhan SARS-CoV-2 with high sensitivity and specificity within five minutes. However, which parts of the virus are recognized by the platform are unknown. Similarly, whether the platform can detect SARS-CoV-2 variants or the presence of the virus in clinical samples needs further study. Here, we demonstrated the platform can distinguish SARS-CoV-2 variants. Further, it identified mutated Wuhan SARS-CoV-2 expressing spike proteins of the delta and omicron variants, indicating it discriminates spike proteins. Finally, we used the platform to identify omicron variants with a sensitivity and specificity of 100% and 94%, respectively, in saliva specimens from COVID-19 patients. Thus, our results demonstrate the AI-nanopore platform is an effective diagnostic tool for SARS-CoV-2 variants.

Lab on a Chip

High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore†

Abstract

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High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore

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