Figure 7.

Patterns of co-occurrence of BA.1 amino-acid residues in circulating SARS-CoV-2 S-gene haplotypes from other lineages (data up to October 15, 2021). Only mutations occurring in at least 10 haplotypes are shown. All sequences having exactly the same S-gene sequence count as a single unique haplotype; instead of counting raw sequence numbers, this approach focuses on the number of unique genetic backgrounds in which pairs of codons co-occur. Circles show odds ratios for finding the mutation on the X axis when the mutation on the Y axis is also present (vs when it is not present). Red circles depict OR > 1, while blue circles 1/OR for OR < 1. Black circles on the right show the fraction of globally sampled SARS-CoV-2 S-gene haplotypes which carry the corresponding mutation.