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

Guan, Qingtian; Sadykov, Mukhtar; Mfarrej, Sara; Hala, Sharif; Naeem, Raeece; Nugmanova, Raushan; Al-Omari, Awad; Salih, Samer; Al Mutair, Abbas; Carr, Michael J.; Hall, William W.; Arold, Stefan T.; Pain, Arnab

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

Guan, Qingtian; Sadykov, Mukhtar; Mfarrej, Sara et al.

International journal of infectious diseases, 2020, 100, 216-223

Permalink : https://hdl.handle.net/2115/80650

このアイテムのアクセス数:717件（2026-08-15 01:44 集計）

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アクセス権	open access
URI	https://hdl.handle.net/2115/80650
タイトル	A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic
著者	Guan, Qingtian ; Sadykov, Mukhtar ; Mfarrej, Sara ; Hala, Sharif ; Naeem, Raeece ; Nugmanova, Raushan ; Al-Omari, Awad ; Salih, Samer ; Al Mutair, Abbas ; Carr, Michael J. ; Hall, William W. ; Arold, Stefan T. ; Pain, Arnab
著者名 Guan, Qingtian
著者名 Sadykov, Mukhtar
著者名 Mfarrej, Sara
著者名 Hala, Sharif
著者名 Naeem, Raeece
著者名 Nugmanova, Raushan
著者名 Al-Omari, Awad
著者名 Salih, Samer
著者名 Al Mutair, Abbas
e-Rad_Researcher 70769588 著者名 Carr, Michael J.
著者名 Hall, William W.
著者名 Arold, Stefan T.
著者名 Pain, Arnab
言語	英語
キーワード	SARS-CoV-2
	Genetic surveillance
	Barcoding
	Genome variation
発行日	2020-11
出版者	Elsevier
収録物名	International journal of infectious diseases
巻(号)	100
ページ	216-223
抄録	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.
資源タイプ	学術雑誌論文
出版タイプ	Version of Record
権利情報	Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
PISSN	1201-9712
関連情報 (isIdenticalTo)	出版社版DOI https://doi.org/10.1016/j.ijid.2020.08.052