A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic
Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved..
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 with 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 11 major mutations which defined five major clades (G614, S84, V251, I378 and D392) of globally circulating viral populations. The clades can specifically identify 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 5 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 decreases in genetic diversity as treatment and vaccine approaches become widely available.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2020 |
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| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:100 |
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| Enthalten in: |
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases - 100(2020) vom: 01. Nov., Seite 216-223 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Guan, Qingtian [VerfasserIn] |
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| Links: |
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| Themen: |
Barcoding |
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| Anmerkungen: |
Date Completed 10.12.2020 Date Revised 12.11.2023 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.ijid.2020.08.052 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 2 | |a A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic |
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| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved. | ||
| 520 | |a 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 with existing comprehensive, albeit though slower, genome sequencing-driven approaches | ||
| 520 | |a 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 | ||
| 520 | |a RESULTS: We describe 11 major mutations which defined five major clades (G614, S84, V251, I378 and D392) of globally circulating viral populations. The clades can specifically identify 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 | ||
| 520 | |a CONCLUSION: Globally circulating SARS-CoV-2 genomes could be classified into 5 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 decreases in genetic diversity as treatment and vaccine approaches become widely available | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a barcoding | |
| 650 | 4 | |a genetic surveillance | |
| 650 | 4 | |a genome variation | |
| 650 | 7 | |a Viral Proteins |2 NLM | |
| 700 | 1 | |a Sadykov, Mukhtar |e verfasserin |4 aut | |
| 700 | 1 | |a Mfarrej, Sara |e verfasserin |4 aut | |
| 700 | 1 | |a Hala, Sharif |e verfasserin |4 aut | |
| 700 | 1 | |a Naeem, Raeece |e verfasserin |4 aut | |
| 700 | 1 | |a Nugmanova, Raushan |e verfasserin |4 aut | |
| 700 | 1 | |a Al-Omari, Awad |e verfasserin |4 aut | |
| 700 | 1 | |a Salih, Samer |e verfasserin |4 aut | |
| 700 | 1 | |a Al Mutair, Abbas |e verfasserin |4 aut | |
| 700 | 1 | |a Carr, Michael J |e verfasserin |4 aut | |
| 700 | 1 | |a Hall, William W |e verfasserin |4 aut | |
| 700 | 1 | |a Arold, Stefan T |e verfasserin |4 aut | |
| 700 | 1 | |a Pain, Arnab |e verfasserin |4 aut | |
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