PT  - JOURNAL ARTICLE
AU  - Ahmed M. Moustafa
AU  - Paul J. Planet
TI  - Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread
AID  - 10.1101/2020.06.08.139055
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.08.139055
4099  - http://biorxiv.org/content/early/2020/06/09/2020.06.08.139055.short
4100  - http://biorxiv.org/content/early/2020/06/09/2020.06.08.139055.full
AB  - 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 StatementThe authors have declared no competing interest.WhatsGNUWhat is Gene Novelty UnitGNUVIDGene Novelty Unit-based Virus IdentificationSTSequence TypeCCClonal ComplexSARS-CoV-2Severe Acute Respiratory Syndrome Corona Virus 2COVID-19Corona Virus Disease 2019MLSTMultilocus Sequence TypingcgMLSTcore genome MLSTwgMLSTwhole genome MLST