Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis

Hajime Shinoda; Tatsuya Iida; Asami Makino; Mami Yoshimura; Junichiro Ishikawa; Jun Ando; Kazue Murai; Katsumi Sugiyama; Yukiko Muramoto; Masahiro Nakano; Kotaro Kiga; Longzhu Cui; Osamu Nureki; Hiroaki Takeuchi; Takeshi Noda; Hiroshi Nishimasu; Rikiya Watanabe

doi:10.1038/s42003-022-03433-6

Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis

Commun Biol. 2022 May 26;5(1):473. doi: 10.1038/s42003-022-03433-6.

Authors

Hajime Shinoda^#^{1

2}, Tatsuya Iida^#^{1

2}, Asami Makino^#^{1

2}, Mami Yoshimura^#^{1

2}, Junichiro Ishikawa³, Jun Ando^{1

2}, Kazue Murai¹, Katsumi Sugiyama⁴, Yukiko Muramoto^{2

5}, Masahiro Nakano^{2

5}, Kotaro Kiga^{6

7}, Longzhu Cui⁶, Osamu Nureki³, Hiroaki Takeuchi⁸, Takeshi Noda^{2

5}, Hiroshi Nishimasu^{9

10

11

12

13}, Rikiya Watanabe^{14

15}

Affiliations

¹ Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.
² CREST, Japan Science and Technology Agency, Saitama, Japan.
³ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
⁴ FUJIFILM Media Crest Co., Ltd, Tokyo, Japan.
⁵ Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
⁶ Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan.
⁷ Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
⁸ Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan.
⁹ CREST, Japan Science and Technology Agency, Saitama, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.
¹⁰ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.
¹¹ Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.
¹² Research Center for Advanced Science and Technology, Structural Biology Division, The University of Tokyo, Tokyo, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.
¹³ Inamori Research Institute for Science, Kyoto, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.
¹⁴ Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan. rikiya.watanabe@riken.jp.
¹⁵ CREST, Japan Science and Technology Agency, Saitama, Japan. rikiya.watanabe@riken.jp.

^# Contributed equally.

Abstract

In the ongoing COVID-19 pandemic, rapid and sensitive diagnosis of viral infection is a critical deterrent to the spread of SARS-CoV-2. To this end, we developed an automated amplification-free digital RNA detection platform using CRISPR-Cas13a and microchamber device (opn-SATORI), which automatically completes a detection process from sample mixing to RNA quantification in clinical specimens within ~9 min. Using the optimal Cas13a enzyme and magnetic beads technology, opn-SATORI detected SARS-CoV-2 genomic RNA with a LoD of < 6.5 aM (3.9 copies μL^-1), comparable to RT-qPCR. Additionally, opn-SATORI discriminated between SARS-CoV-2 variants of concern, including alpha, delta, and omicron, with 98% accuracy. Thus, opn-SATORI can serve as a rapid and convenient diagnostic platform for identifying several types of viral infections.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 Testing
COVID-19* / diagnosis
Humans
Pandemics
RNA, Viral / genetics
SARS-CoV-2* / genetics

Substances

RNA, Viral

Supplementary concepts

SARS-CoV-2 variants