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

• Published in: International journal of infectious diseases Vol. 100; pp. 216 - 223
• Main Authors: Guan, Qingtian, Sadykov, Mukhtar, Mfarrej, Sara, Hala, Sharif, Naeem, Raeece, Nugmanova, Raushan, Al-Omari, Awad, Salih, Samer, Mutair, Abbas Al, Carr, Michael J., Hall, William W., Arold, Stefan T., Pain, Arnab
• Format: Journal Article
• Language: English
• Published: Canada Elsevier Ltd 01.11.2020; The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases; Elsevier
• Subjects: Barcoding; COVID-19 - epidemiology; COVID-19 - virology; Genetic surveillance; Genome variation; Genome, Viral; High-Throughput Nucleotide Sequencing; Humans; Molecular Typing; Mutation; Pandemics; SARS-CoV-2; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; Viral Proteins - genetics; barcoding; genetic surveillance; SARS-CoV-2; genome variation
• ISSN: 1201-9712; 1878-3511
• DOI: 10.1016/j.ijid.2020.08.052

•We describe 11 major mutation events which defined five major clades (G614, S84, V251, I378 and D392) of globally-circulating viral populations.•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.•Several nonsynonymous mutations in the spike protein may have functional consequences: the G clade–defining mutation D614 G located in subdomain 1; the V367 F, G476S and V483A are localised in the receptor binding domain (RBD) of the spike protein. 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. 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. 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. 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.