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A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic

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Title: A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic
Authors: Guan, Qingtian Browse this author
Sadykov, Mukhtar Browse this author
Mfarrej, Sara Browse this author
Hala, Sharif Browse this author
Naeem, Raeece Browse this author
Nugmanova, Raushan Browse this author
Al-Omari, Awad Browse this author
Salih, Samer Browse this author
Al Mutair, Abbas Browse this author
Carr, Michael J. Browse this author →KAKEN DB
Hall, William W. Browse this author
Arold, Stefan T. Browse this author
Pain, Arnab Browse this author
Keywords: SARS-CoV-2
Genetic surveillance
Genome variation
Issue Date: Nov-2020
Publisher: Elsevier
Journal Title: International journal of infectious diseases
Volume: 100
Start Page: 216
End Page: 223
Publisher DOI: 10.1016/j.ijid.2020.08.052
Abstract: Objective: The SARS-CoV-2 pathogen has established endemicity in humans. This necessitates the development of rapid genetic surveillance methodologies to serve as an adjunct to existing comprehensive, albeit though slower, genome sequencing-driven approaches. Methods: A total of 21,789 complete genomes were downloaded from GISAID on May 28, 2020, for analyses. We have defined the major clades and subclades of circulating SARS-CoV-2 genomes. A rapid sequencing-based genotyping protocol was developed and tested on SARS-CoV-2-positive RNA samples by next-generation sequencing. Results: We describe eleven major mutation events that defined five major clades (G(614), S-84, V-251, I-378, and D-392) of globally-circulating viral populations. The clades can be specifically identified using an 11-nucleotide genetic barcode. An analysis of amino acid variation in SARS-CoV-2 proteins provided evidence of substitution events in the viral proteins involved in both host entry and genome replication. Conclusion: Globally-circulating SARS-CoV-2 genomes could be classified into five major clades based on mutational profiles defined by an 11-nucleotide barcode. We have successfully developed a multiplexed sequencing-based, rapid genotyping protocol for high-throughput classification of major clade types of SARS-CoV-2 in clinical samples. This barcoding strategy will be required to monitor genetic diversity decrease as treatment and vaccine approaches become widely available. (C) 2020 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.
Type: article
Appears in Collections:国際連携機構 (Institute for International Collaboration) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

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