ahmedmagds/GNUVID: GNUVID v1.2: Globally circulating clonal complexes as of 2020-06-17
Description
Summary
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18298 GISAID sequences have been included in this analysis.
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GNUVID compressed the 182980 ORFs in the 18298 genomes to 10686 unique alleles.
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9676 Sequence Types (STs) have been assigned in this dataset and were clustered in 45 clonal complexes (CCs).
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21 new CCs have been assigned.
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33 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-06-17).
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5 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-06-17).
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7 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-06-17).
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CC70 and CC26 have now been called CC550 and CC750, respectively.
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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.
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Beijing/IVDC-01-06/2020|EPI_ISL_469254|2020-06-11 is assigned to ST9646 (CC300)
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Beijing/IVDC-02-06/2020|EPI_ISL_469255|2020-06-11 is assigned to ST9647 (CC300)
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Beijing/env/IVDC-03-06/2020|EPI_ISL_469256|2020-06-11 is assigned to ST9648 (CC300)
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Files
ahmedmagds/GNUVID-v1.2.zip
Files
(33.7 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/ahmedmagds/GNUVID/tree/v1.2 (URL)