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dc.contributor.authorGuan, Qingtian
dc.contributor.authorSadykov, Mukhtar
dc.contributor.authorNugmanova, Raushan
dc.contributor.authorCarr, Michael J
dc.contributor.authorArold, Stefan T.
dc.contributor.authorPain, Arnab
dc.date.accessioned2020-04-26T09:54:25Z
dc.date.available2020-04-26T09:54:25Z
dc.date.issued2020-04-23
dc.identifier.citationGuan, Q., Sadykov, M., Nugmanova, R., Carr, M. J., Arold, S. T., & Pain, A. (2020). The genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme. doi:10.1101/2020.04.21.054221
dc.identifier.doi10.1101/2020.04.21.054221
dc.identifier.urihttp://hdl.handle.net/10754/662635
dc.description.abstractWe describe fifteen major mutation events from 2,058 high-quality SARS-CoV-2 genomes deposited up to March 31st, 2020. These events define five major clades (G, I, S, D and V) of globally-circulating viral populations, representing 85.7% of all sequenced cases, which we can identify using a 10 nucleotide genetic classifier or barcode. We applied this barcode to 4,000 additional genomes deposited between March 31st and April 15th and classified successfully 95.6% of the clades demonstrating the utility of this approach. An analysis of amino acid variation in SARS-CoV-2 ORFs provided evidence of substitution events in the viral proteins involved in both host-entry and genome replication. The systematic monitoring of dynamic changes in the SARS-CoV-2 genomes of circulating virus populations over time can guide therapeutic and prophylactic strategies to manage and contain the virus and, also, with available efficacious antivirals and vaccines, aid in the monitoring of circulating genetic diversity as we proceed towards elimination of the agent. The barcode will add the necessary genetic resolution to facilitate tracking and monitoring of infection clusters to distinguish imported and indigenous cases and thereby aid public health measures seeking to interrupt transmission chains without the requirement for real-time complete genomes sequencing.
dc.description.sponsorshipThis work was supported by funding from King Abdullah University of Science and Technology (KAUST), Office of Sponsored Research (OSR), under award number FCC/1/1976-25-01. Work in AP’s laboratory is supported by the KAUST faculty baseline fund (BAS/1/1020-01- 01) and research grants from the Office for Sponsored Research (OSR-2015-CRG4-2610, OCRF-2014-CRG3-2267). We thank all laboratories which have contributed sequences to the GISAID database. We thank Olga Douvropoulou, Raeece Naeem Mohamed Ghazzali and Sharif Hala for their 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.publisherCold Spring Harbor Laboratory
dc.relation.urlhttp://biorxiv.org/lookup/doi/10.1101/2020.04.21.054221
dc.relation.urlhttps://www.biorxiv.org/content/biorxiv/early/2020/04/23/2020.04.21.054221.full.pdf
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory
dc.titleThe genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme
dc.typePreprint
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.departmentEnvironmental Science and Engineering Program
dc.contributor.departmentKing Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal8 Jeddah, 23955-6900, Saudi Arabia.
dc.contributor.departmentPathogen Genomics Laboratory
dc.contributor.departmentStructural Biology and Engineering
dc.eprint.versionPre-print
dc.contributor.institutionNational Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin 4, 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.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.personNugmanova, Raushan
kaust.personArold, Stefan T.
kaust.personPain, Arnab
kaust.grant.numberFCC/1/1976-25-01
kaust.grant.numberOCRF-2014-CRG3-2267
kaust.grant.numberOSR-2015-CRG4-2610
refterms.dateFOA2020-04-26T09:55:39Z
kaust.acknowledged.supportUnitOffice of Sponsored Research (OSR)


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