دورية أكاديمية
أعرض في EDS

Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness.

التفاصيل البيبلوغرافية
العنوان: Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness.
المؤلفون: Carbo EC; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands. Electronic address: e.c.carbo@lumc.nl., Sidorov IA; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands., Zevenhoven-Dobbe JC; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands., Snijder EJ; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands., Claas EC; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands., Laros JFJ; Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands; National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands., Kroes ACM; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands., de Vries JJC; Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, the Netherlands.
المصدر: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology [J Clin Virol] 2020 Oct; Vol. 131, pp. 104594. Date of Electronic Publication: 2020 Aug 21.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier Science Country of Publication: Netherlands NLM ID: 9815671 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-5967 (Electronic) Linking ISSN: 13866532 NLM ISO Abbreviation: J Clin Virol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Amsterdam : Elsevier Science, c1998-
مواضيع طبية MeSH: Genome, Viral* , High-Throughput Nucleotide Sequencing* , Metagenomics*, Coronavirus Infections/*virology , Pneumonia, Viral/*virology, Betacoronavirus/isolation & purification ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Computational Biology ; Coronavirus Infections/diagnosis ; Humans ; Middle East Respiratory Syndrome Coronavirus/isolation & purification ; Nasopharynx/virology ; Pandemics ; Severe acute respiratory syndrome-related coronavirus/isolation & purification ; SARS-CoV-2
مستخلص: Introduction: The SARS-CoV-2 pandemic of 2020 is a prime example of the omnipresent threat of emerging viruses that can infect humans. A protocol for the identification of novel coronaviruses by viral metagenomic sequencing in diagnostic laboratories may contribute to pandemic preparedness.
Aim: The aim of this study is to validate a metagenomic virus discovery protocol as a tool for coronavirus pandemic preparedness.
Methods: The performance of a viral metagenomic protocol in a clinical setting for the identification of novel coronaviruses was tested using clinical samples containing SARS-CoV-2, SARS-CoV, and MERS-CoV, in combination with databases generated to contain only viruses of before the discovery dates of these coronaviruses, to mimic virus discovery.
Results: Classification of NGS reads using Centrifuge and Genome Detective resulted in assignment of the reads to the closest relatives of the emerging coronaviruses. Low nucleotide and amino acid identity (81% and 84%, respectively, for SARS-CoV-2) in combination with up to 98% genome coverage were indicative for a related, novel coronavirus. Capture probes targeting vertebrate viruses, designed in 2015, enhanced both sequencing depth and coverage of the SARS-CoV-2 genome, the latter increasing from 71% to 98%.
Conclusion: The model used for simulation of virus discovery enabled validation of the metagenomic sequencing protocol. The metagenomic protocol with virus probes designed before the pandemic, can assist the detection and identification of novel coronaviruses directly in clinical samples.
(Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)
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فهرسة مساهمة: Keywords: COVID-19; SARS-CoV-2; bioinformatics; metagenomics; virus discovery
تواريخ الأحداث: Date Created: 20200901 Date Completed: 20201005 Latest Revision: 20221207
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC7441049
DOI: 10.1016/j.jcv.2020.104594
PMID: 32866812
قاعدة البيانات: MEDLINE
الوصف
تدمد:1873-5967
DOI:10.1016/j.jcv.2020.104594