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Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses.
Small. 2020 08; 16(32):e2002169.S

Abstract

The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens.

Authors+Show Affiliations

Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.Department of Internal Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China.CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200040, China.Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.

Pub Type(s)

Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32578378

Citation

Wang, Ming, et al. "Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses." Small (Weinheim an Der Bergstrasse, Germany), vol. 16, no. 32, 2020, pp. e2002169.
Wang M, Fu A, Hu B, et al. Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses. Small. 2020;16(32):e2002169.
Wang, M., Fu, A., Hu, B., Tong, Y., Liu, R., Liu, Z., Gu, J., Xiang, B., Liu, J., Jiang, W., Shen, G., Zhao, W., Men, D., Deng, Z., Yu, L., Wei, W., Li, Y., & Liu, T. (2020). Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses. Small (Weinheim an Der Bergstrasse, Germany), 16(32), e2002169. https://doi.org/10.1002/smll.202002169
Wang M, et al. Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses. Small. 2020;16(32):e2002169. PubMed PMID: 32578378.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses. AU - Wang,Ming, AU - Fu,Aisi, AU - Hu,Ben, AU - Tong,Yongqing, AU - Liu,Ran, AU - Liu,Zhen, AU - Gu,Jiashuang, AU - Xiang,Bin, AU - Liu,Jianghao, AU - Jiang,Wen, AU - Shen,Gaigai, AU - Zhao,Wanxu, AU - Men,Dong, AU - Deng,Zixin, AU - Yu,Lilei, AU - Wei,Wu, AU - Li,Yan, AU - Liu,Tiangang, Y1 - 2020/06/24/ PY - 2020/04/03/received PY - 2020/05/27/revised PY - 2020/6/25/pubmed PY - 2020/8/28/medline PY - 2020/6/25/entrez KW - COVID-19 KW - SARS-CoV-2 KW - nanopore sequencing KW - respiratory virus KW - targeted amplification SP - e2002169 EP - e2002169 JF - Small (Weinheim an der Bergstrasse, Germany) JO - Small VL - 16 IS - 32 N2 - The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens. SN - 1613-6829 UR - https://www.unboundmedicine.com/medline/citation/32578378/Nanopore_Targeted_Sequencing_for_the_Accurate_and_Comprehensive_Detection_of_SARS_CoV_2_and_Other_Respiratory_Viruses_ L2 - https://doi.org/10.1002/smll.202002169 DB - PRIME DP - Unbound Medicine ER -