(A) Frequency plot showing the number of SARS-CoV-2 sequences per week for VOCs
Alpha, Delta, Delta-AY4.2, Omicron BA.1 and BA.2, and ‘other’ pre-VOC variants (see
key) in the UK. The light grey box covering the two most recent weeks indicates a
period in which sequence counts are low due to a lag (Figure S1). (B) Spike protein
structure showing locations of Delta- and Omicron-specific spike mutations. Ectodomain
of the spike homotrimer in open conformation with individual spike protein chains
shown in different colours. On each monomer, highlighted spheres show the locations of
amino acid substitutions, deletions (Δ), or insertions (ins) that distinguish the
Omicron (BA.1) variant, relative to the original genotype (Wuhan-Hu-1). These are
annotated on the monomer with an ‘up’ receptor-binding domain where they are
highlighted in red on teal. The substitution D614G, which is shared by common descent
by all lineage B.1 descendants is italicised. The visualisation is made using a
complete spike model (Woo et al. 2020), which
is in turn based upon a partial cryo-EM structure (RCSB Protein Data Bank (PDB) ID:
6VSB (Wrapp et al. 2020)).