Software Open Access
Ahmed M Moustafa
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)