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Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread

View ORCID ProfileAhmed M. Moustafa, View ORCID ProfilePaul J. Planet
doi: https://doi.org/10.1101/2020.06.08.139055
Ahmed M. Moustafa
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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  • ORCID record for Ahmed M. Moustafa
Paul J. Planet
1Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
2Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
3Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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  • For correspondence: planetp@email.chop.edu
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Abstract

As the pandemic SARS-CoV-2 virus has spread globally its genome has diversified to an extent that distinct clones can now be recognized, tracked, and traced. Identifying clonal groups allows for assessment of geographic spread, transmission events, and identification of new or emerging strains that may be more virulent or more transmissible. Here we present a rapid, whole genome, allele-based method (GNUVID) for assigning sequence types to sequenced isolates of SARS-CoV-2 sequences. This sequence typing scheme can be updated with new genomic information extremely rapidly, making our technique continually adaptable as databases grow. We show that our method is consistent with phylogeny and recovers waves of expansion and replacement of sequence types/clonal complexes in different geographical locations.

GNUVID is available as a command line application (https://github.com/ahmedmagds/GNUVID).

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Emails AMM: moustafaam{at}email.chop.edu

  • https://github.com/ahmedmagds/GNUVID

  • List of abbreviations

    WhatsGNU
    What is Gene Novelty Unit
    GNUVID
    Gene Novelty Unit-based Virus Identification
    ST
    Sequence Type
    CC
    Clonal Complex
    SARS-CoV-2
    Severe Acute Respiratory Syndrome Corona Virus 2
    COVID-19
    Corona Virus Disease 2019
    MLST
    Multilocus Sequence Typing
    cgMLST
    core genome MLST
    wgMLST
    whole genome MLST
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted June 09, 2020.
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    Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread
    Ahmed M. Moustafa, Paul J. Planet
    bioRxiv 2020.06.08.139055; doi: https://doi.org/10.1101/2020.06.08.139055
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    Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread
    Ahmed M. Moustafa, Paul J. Planet
    bioRxiv 2020.06.08.139055; doi: https://doi.org/10.1101/2020.06.08.139055

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