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Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses.
Wang, Ming; Fu, Aisi; Hu, Ben; Tong, Yongqing; Liu, Ran; Liu, Zhen; Gu, Jiashuang; Xiang, Bin; Liu, Jianghao; Jiang, Wen; Shen, Gaigai; Zhao, Wanxu; Men, Dong; Deng, Zixin; Yu, Lilei; Wei, Wu; Li, Yan; Liu, Tiangang.
  • Wang M; Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
  • Fu A; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Hu B; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Tong Y; Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
  • Liu R; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Liu Z; 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.
  • Gu J; Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.
  • Xiang B; 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.
  • Liu J; Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.
  • Jiang W; Wuhan Dgensee Clinical Laboratory Co., Ltd., Wuhan, 430075, China.
  • Shen G; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Zhao W; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Men D; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
  • Deng Z; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China.
  • Yu L; Department of Internal Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
  • Wei W; 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.
  • Li Y; 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.
  • Liu T; Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
Small ; 16(32): e2002169, 2020 08.
Article in English | MEDLINE | ID: covidwho-612774
Semantic information from SemMedBD (by NLM)
1. Misdiagnosis PROCESS_OF Patients
Subject
Misdiagnosis
Predicate
PROCESS_OF
Object
Patients
2. Nucleic acid assay NEG_DIAGNOSES Respiratory viruses
Subject
Nucleic acid assay
Predicate
NEG_DIAGNOSES
Object
Respiratory viruses
3. Nanopore Sequencing DIAGNOSES Respiratory viruses
Subject
Nanopore Sequencing
Predicate
DIAGNOSES
Object
Respiratory viruses
4. Nanopore Sequencing DIAGNOSES 2019 novel coronavirus
Subject
Nanopore Sequencing
Predicate
DIAGNOSES
Object
2019 novel coronavirus
5. Respiratory viruses INTERACTS_WITH 2019 novel coronavirus
Subject
Respiratory viruses
Predicate
INTERACTS_WITH
Object
2019 novel coronavirus
6. Infected PROCESS_OF Patients
Subject
Infected
Predicate
PROCESS_OF
Object
Patients
7. Nucleic acid specimen PART_OF Patients
Subject
Nucleic acid specimen
Predicate
PART_OF
Object
Patients
8. Misdiagnosis PROCESS_OF Patients
Subject
Misdiagnosis
Predicate
PROCESS_OF
Object
Patients
9. Nucleic acid assay NEG_DIAGNOSES Respiratory viruses
Subject
Nucleic acid assay
Predicate
NEG_DIAGNOSES
Object
Respiratory viruses
10. Nanopore Sequencing DIAGNOSES Respiratory viruses
Subject
Nanopore Sequencing
Predicate
DIAGNOSES
Object
Respiratory viruses
11. Nanopore Sequencing DIAGNOSES 2019 novel coronavirus
Subject
Nanopore Sequencing
Predicate
DIAGNOSES
Object
2019 novel coronavirus
12. Respiratory viruses INTERACTS_WITH 2019 novel coronavirus
Subject
Respiratory viruses
Predicate
INTERACTS_WITH
Object
2019 novel coronavirus
13. Infected PROCESS_OF Patients
Subject
Infected
Predicate
PROCESS_OF
Object
Patients
14. Nucleic acid specimen PART_OF Patients
Subject
Nucleic acid specimen
Predicate
PART_OF
Object
Patients
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.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Coronavirus Infections / Nucleic Acid Amplification Techniques / Nanopores / Betacoronavirus Type of study: Diagnostic study / Evaluation study / Prognostic study Topics: Long Covid Limits: Humans Language: English Journal: Small Journal subject: Biomedical Engineering Year: 2020 Document Type: Article Affiliation country: Smll.202002169

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / Coronavirus Infections / Nucleic Acid Amplification Techniques / Nanopores / Betacoronavirus Type of study: Diagnostic study / Evaluation study / Prognostic study Topics: Long Covid Limits: Humans Language: English Journal: Small Journal subject: Biomedical Engineering Year: 2020 Document Type: Article Affiliation country: Smll.202002169