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

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

doi:10.1016/j.ijid.2020.08.052

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

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

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

Abstract

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.

Original language	English (US)
Journal	International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
DOIs	https://doi.org/10.1016/j.ijid.2020.08.052
State	Published - Aug 26 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We 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.

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10.1016/j.ijid.2020.08.052

https://repository.kaust.edu.sa/bitstream/10754/664853/1/Genetic_1-s2.0-S1201971220306810-main.pdf

Cite this

Guan, Q., Sadykov, M., Mfarrej, S., Hala, S., Naeem, R., Nugmanova, R., Al-Omari, A., Salih, S., Mutair, A. A., Carr, M. J., Hall, W. W., Arold, S. T., & 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 : IJID : official publication of the International Society for Infectious Diseases. https://doi.org/10.1016/j.ijid.2020.08.052

@article{717f2d4941cc4a83ac44fc86dab7465d,

title = "A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.",

abstract = "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.",

author = "Qingtian Guan and Mukhtar Sadykov and Sara Mfarrej and Sharif Hala and Raeece Naeem and Raushan Nugmanova and Awad Al-Omari and Samer Salih and Mutair, {Abbas Al} and Carr, {Michael J} and Hall, {William W} and Arold, {Stefan T.} and Arnab Pain",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We 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.",

year = "2020",

month = aug,

day = "26",

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journal = "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases",

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Guan, Q, Sadykov, M , Mfarrej, S, Hala, S, Naeem, R, Nugmanova, R, Al-Omari, A, Salih, S, Mutair, AA, Carr, MJ, Hall, WW, Arold, ST & 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 : IJID : official publication of the International Society for Infectious Diseases. https://doi.org/10.1016/j.ijid.2020.08.052

A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. / Guan, Qingtian; Sadykov, Mukhtar ; Mfarrej, Sara et al.
In: International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 26.08.2020.

Research output: Contribution to journal › Article › peer-review

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T1 - A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.

AU - Guan, Qingtian

AU - Sadykov, Mukhtar

AU - Mfarrej, Sara

AU - Hala, Sharif

AU - Naeem, Raeece

AU - Nugmanova, Raushan

AU - Al-Omari, Awad

AU - Salih, Samer

AU - Mutair, Abbas Al

AU - Carr, Michael J

AU - Hall, William W

AU - Arold, Stefan T.

AU - Pain, Arnab

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We 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.

PY - 2020/8/26

Y1 - 2020/8/26

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/664853

UR - https://linkinghub.elsevier.com/retrieve/pii/S1201971220306810

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DO - 10.1016/j.ijid.2020.08.052

M3 - Article

C2 - 32841689

SN - 1201-9712

JO - International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

JF - International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

ER -

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

Abstract

Bibliographical note

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