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. 2021 Aug 26;10:e70658. doi: 10.7554/eLife.70658

Figure 1. Spike RBD and ACE2 variants analysed in this study.

(A) Phylogenetic tree illustrating the clades containing the RBD mutations investigated in this study. Constructed using TreeTime (Sagulenko et al., 2018) from the Nextstrain Global (Hadfield et al., 2018) sample of SARS-CoV-2 sequences from the GISAID database (Shu and McCauley, 2017) (accessed 15 April 2021, N = 4017). (B) Alignment illustrating the Spike residues that differ between SARS-CoV-2 variants, with the RBD mutants boxed. The variants are labelled with their clade designation from Nextstrain (Hadfield et al., 2018) and/or PANGO lineage (Rambaut et al., 2020), where relevant. The RBD mutations were collated from CoVariants (Hodcroft, 2021) and Nextstrain. (C) The structure of human ACE2 (green) in complex with SARS-CoV-2 Spike RBD (cyan). The area enclosed by the box is shown enlarged on the right, with the residues mutated in this study labelled. Drawn using UCSF Chimera (Pettersen et al., 2004) using coordinates from PDB 6m0j (Lan et al., 2020).

Figure 1.

Figure 1—figure supplement 1. Emergence of the same RBD mutations in multiple SAR2-CoV-2 clades.

Figure 1—figure supplement 1.

The figure highlights the SARS-CoV-2 clades containing RBD mutations investigated in this study. The phylogenetic trees were constructed as in Figure 1A from SARS-CoV-2 sequences accessed on 22 April 2021 (N = 3914). (A) N501Y has emerged independently in the three clades 501Y.V1, 501Y.V2, and 501Y.V3. Mutation to T at this position has also occurred frequently. (B) E484K has also been observed independently of its main progenitor clades 501Y.V2 and 501Y.V3. E484Q and E484G have also been observed. (C) S477N has been observed beyond clades 20 F and 20A.EU2. Mutations to I and R have also been occasionally observed at this position. (D) Mutations of K417 to N and T have been observed almost exclusively in the 20 H.501Y.V2 and 20 J.501Y.V3 clades.