| Autor: |
Qingtian Guan, Mukhtar Sadykov, Sara Mfarrej, Sharif Hala, Raeece Naeem, Raushan Nugmanova, Awad Al-Omari, Samer Salih, Abbas Al Mutair, Michael J. Carr, William W. Hall, Stefan T. Arold, Arnab Pain |
| Jazyk: |
angličtina |
| Rok vydání: |
2020 |
| Předmět: |
|
| Zdroj: |
International Journal of Infectious Diseases, Vol 100, Iss , Pp 216-223 (2020) |
| Druh dokumentu: |
article |
| ISSN: |
1201-9712 |
| DOI: |
10.1016/j.ijid.2020.08.052 |
| Popis: |
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 (G614, S84, V251, I378, and D392) 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. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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