ahmedmagds/GNUVID: GNUVID v2.1: Globally circulating clonal complexes as of 2021-01-06 (Variants of Concern now being assigned)

GNUVID 2.1 GNUVID now assigns the three new variants of concern (UK, SA and Brazilian):

• CC81085 represents the Brazilian P.1 lineage (a.k.a. 20J/501Y.V3).
• CC71014 represents the South African B.1.351 lineage (a.k.a. 20H/501Y.V2).
• 10 CCs represent the UK B.1.1.7 lineage (a.k.a. 20I/501Y.V1 Variant of Concern (VOC) 202012/01). (10 CCs: 46649, 45062, 49676, 54949, 54452, 58534, 57630, 66559, 62415 and 67441).

• 159515 GISAID sequences have been included in this analysis.

• GNUVID compressed the 1595150 ORFs in the 159515 genomes to 89491 unique alleles.

• 81097 Sequence Types (STs) have been assigned in this dataset and were clustered in 406 clonal complexes (CCs).

• 252 new CCs have been assigned.

• 133 CCs have been Inactive (i.e. Last time seen more than 1 month before 2021-01-06).

• 209 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2021-01-06).

• 64 CCs have been Active (i.e. Last seen within the 2 weeks before 2021-01-06).