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ahmedmagds/GNUVID: Globally circulating clonal complexes as of 2020-06-17

Ahmed M Moustafa

Summary:

  • 18298 GISAID sequences have been included in this analysis.

  • GNUVID compressed the 182980 ORFs in the 18298 genomes to 10686 unique alleles.

  • 9676 Sequence Types (STs) have been assigned in this dataset and were clustered in 45 clonal complexes (CCs).

  • 21 new CCs have been assigned.

  • 33 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-06-17).

  • 5 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-06-17).

  • 7 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-06-17).

  • CC70 and CC26 have now been called CC550 and CC750, respectively.

  • The three Beijing isolates that are from the recent Beijing's big new COVID-19 outbreak were assigned three new STs that are all Single Locus Variant (SLV) at ORF1ab of ST300, that is mainly found in Europe and founder of CC300.

    • Beijing/IVDC-01-06/2020|EPI_ISL_469254|2020-06-11 is assigned to ST9646 (CC300)

    • Beijing/IVDC-02-06/2020|EPI_ISL_469255|2020-06-11 is assigned to ST9647 (CC300)

    • Beijing/env/IVDC-03-06/2020|EPI_ISL_469256|2020-06-11 is assigned to ST9648 (CC300)

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