A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.
Int J Infect Dis
; 100: 216-223, 2020 Nov.
Article
in En
| MEDLINE
| ID: mdl-32841689
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 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.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Genome, Viral
/
Molecular Typing
/
SARS-CoV-2
/
COVID-19
Type of study:
Guideline
Limits:
Humans
Language:
En
Journal:
Int J Infect Dis
Journal subject:
DOENCAS TRANSMISSIVEIS
Year:
2020
Document type:
Article
Affiliation country:
Saudi Arabia