A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.
Mutair, Abbas Al
Carr, Michael J
Hall, William W
Arold, Stefan T.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Pathogen Genomics Laboratory
Structural Biology and Engineering
Online Publication Date2020-08-22
Print Publication Date2020-11
Permanent link to this recordhttp://hdl.handle.net/10754/664853
MetadataShow full item record
AbstractThe 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.
CitationGuan, Q., Sadykov, M., Mfarrej, S., Hala, S., Naeem, R., Nugmanova, R., … Pain, A. (2020). A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. International Journal of Infectious Diseases. doi:10.1016/j.ijid.2020.08.052
SponsorsWe are deeply grateful to all laboratories contributing genomic data and metadata to GISAID and nextstrain.org databases. We thank KAUST Rapid Research Response Team (R3T) for supporting our research. We thank Olga Douvropoulou for her support during the work. We also thank Richard Culleton (Nagasaki University, Japan) and Gabo Gonzalez (UCD, Ireland) for their critical comments on the manuscript draft.
- High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
- Authors: Bhoyar RC, Jain A, Sehgal P, Divakar MK, Sharma D, Imran M, Jolly B, Ranjan G, Rophina M, Sharma S, Siwach S, Pandhare K, Sahoo S, Sahoo M, Nayak A, Mohanty JN, Das J, Bhandari S, Mathur SK, Kumar A, Sahlot R, Rojarani P, Lakshmi JV, Surekha A, Sekhar PC, Mahajan S, Masih S, Singh P, Kumar V, Jose B, Mahajan V, Gupta V, Gupta R, Arumugam P, Singh A, Nandy A, P V R, Jha RM, Kumari A, Gandotra S, Rao V, Faruq M, Kumar S, Reshma G B, Varma G N, Roy SS, Sengupta A, Chattopadhyay S, Singhal K, Pradhan S, Jha D, Naushin S, Wadhwa S, Tyagi N, Poojary M, Scaria V, Sivasubbu S
- Issue date: 2021
- Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends.
- Authors: Potdar V, Vipat V, Ramdasi A, Jadhav S, Pawar-Patil J, Walimbe A, Patil SS, Choudhury ML, Shastri J, Agrawal S, Pawar S, Lole K, Abraham P, Cherian S, ICMR-NIV NIC Team
- Issue date: 2021 Jan & Feb
- Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan.
- Authors: Ghanchi NK, Nasir A, Masood KI, Abidi SH, Mahmood SF, Kanji A, Razzak S, Khan W, Shahid S, Yameen M, Raza A, Ashraf J, Ansar Z, Dharejo MB, Islam N, Hasan Z, Hasan R
- Issue date: 2021
- Genomic variation and epidemiology of SARS-CoV-2 importation and early circulation in Israel.
- Authors: Zuckerman NS, Bucris E, Drori Y, Erster O, Sofer D, Pando R, Mendelson E, Mor O, Mandelboim M
- Issue date: 2021
- COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest.
- Authors: Chen AT, Altschuler K, Zhan SH, Chan YA, Deverman BE
- Issue date: 2021 Feb 23