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. 2022 Jul 9;94(10):4830–4838. doi: 10.1002/jmv.27939

Figure 1.

Figure 1

Multiple recombination events of the Delta–Omicron XD. (A) Phylogenetic analysis of the first reported sequence of Delta–Omicron XD by Institut Pasteur has been compared with VOCs, VOIs, and Omicron major subvariants using ML with 1000 bootstrap replicate. (B) Recombination analysis using Delta–Omicron XD as the background template. Recombination events against Omicron BA.1 are highlighted in light blue, and recombination events against Delta are highlighted in light orange. (C) Graphical illustration of amino acid comparison between Delta–Omicron XD, Delta, and Omicron BA.1, emphasizing Spike gene. Similar shared amino acid mutations were grouped and highlighted in orange (Delta–Omicron XD and Delta) and blue (Delta‐Omicron XD and Omicron BA.1). (D) Shared mutations were illustrated using Omicron BA.1 Spike structure (PDB: 7TB4). Regions in the Spike protein were highlighted for NTD (red), RBD (green), and S2 (grey). (E) Pairwise amino acid and nucleotide comparisons of shared mutations were illustrated between Delta–Omicron XD, Delta, and Omicron BA.1. Potential sites or ranges of recombination were depicted using black arrows. ML, maximum likelihood; VOCs, variants of concerns; VOIs, variants of interest.