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dc.contributor.authorGuan, Qingtian
dc.contributor.authorSadykov, Mukhtar
dc.contributor.authorMfarrej, Sara
dc.contributor.authorHala, Sharif
dc.contributor.authorNaeem, Raeece
dc.contributor.authorNugmanova, Raushan
dc.contributor.authorAl-Omari, Awad
dc.contributor.authorSalih, Samer
dc.contributor.authorMutair, Abbas Al
dc.contributor.authorCarr, Michael J
dc.contributor.authorHall, William W
dc.contributor.authorArold, Stefan T.
dc.contributor.authorPain, Arnab
dc.date.accessioned2020-08-27T07:02:23Z
dc.date.available2020-08-27T07:02:23Z
dc.date.issued2020-08-22
dc.date.submitted2020-06-04
dc.identifier.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
dc.identifier.issn1201-9712
dc.identifier.pmid32841689
dc.identifier.doi10.1016/j.ijid.2020.08.052
dc.identifier.urihttp://hdl.handle.net/10754/664853
dc.description.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.
dc.description.sponsorshipWe 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.
dc.publisherElsevier BV
dc.relation.urlhttps://linkinghub.elsevier.com/retrieve/pii/S1201971220306810
dc.rightsThis is an open access article.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.titleA genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentPathogen Genomics Laboratory
dc.contributor.departmentR&F Operations
dc.contributor.departmentStructural Biology and Engineering
dc.identifier.journalInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionSchool of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
dc.contributor.institutionDr.Suliman Al-Habib Medical group, Riyadh, Saudi Arabia.
dc.contributor.institutionNational Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, D04 V1W8, Dublin, Ireland.
dc.contributor.institutionResearch Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020 Japan.
dc.contributor.institutionGlobal Virus Network (GVN), 801 W. Baltimore St., Baltimore, MD, 21201, USA.
dc.contributor.institutionCentre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France.
dc.contributor.institutionNuffield Division of Clinical Laboratory Sciences (NDCLS), The John Radcliffe Hospital, University of Oxford, Headington, Oxford, OX3 9DU, United Kingdom.
kaust.personGuan, Qingtian
kaust.personSadykov, Mukhtar
kaust.personMfarrej, Sara
kaust.personHala, Sharif
kaust.personNaeem, Raeece
kaust.personNugmanova, Raushan
kaust.personArold, Stefan T.
kaust.personPain, Arnab
dc.date.accepted2020-08-18
refterms.dateFOA2020-08-27T07:04:19Z
dc.date.published-online2020-08-22
dc.date.published-print2020-11


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