New proposed lineage
By Tom Peacock
Description
Sub-lineage of: B.1.1
Earliest Sequence: 2021-11-11
Latest Sequence: 2021-11-13
Countries circulating: Botswana (3 genomes), Hong Kong ex S. Africa (1 genome, partial)
Description:
Conserved Spike mutations - A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
Conserved non-Spike mutations - NSP3 – K38R, V1069I, Δ1265/L1266I, A1892T; NSP4 – T492I; NSP5 – P132H; NSP6 – Δ105-107, A189V; NSP12 – P323L; NSP14 – I42V; E – T9I; M – D3G, Q19E, A63T; N – P13L, Δ31-33, R203K, G204R
Currently only 4 sequences so would recommend monitoring for now. Export to Asia implies this might be more widespread than sequences alone would imply. Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies)
Genomes:
EPI_ISL_6590608 (partial RBD Sanger sequencing from Hong Kong)
EPI_ISL_6640916
EPI_ISL_6640919
EPI_ISL_6640917
Evidence:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_17ae0_cf96f0.json
Proposed lineage name: B.1.1.X