As a result, we concluded that the formation of a part of Omicron isolates BA.1, BA.1.1, and BA.2 was not the product of genome evolution, as is commonly observed in nature, such as the accumulation of mutations and homologous recombinations. Furthermore, the study of 35 recombinant isolates of Omicron variants BA.1 and BA.2...
This is missing the biggest piece: phylogenetic analysis. They aligned a selected group of mutations and then eyeballed the alignments and then speculated.
Unnatural evolutionary processes of SARS-CoV-2 variants and possibility of deliberate natural selection (zenodo.org)
As a result, we concluded that the formation of a part of Omicron isolates BA.1, BA.1.1, and BA.2 was not the product of genome evolution, as is commonly observed in nature, such as the accumulation of mutations and homologous recombinations. Furthermore, the study of 35 recombinant isolates of Omicron variants BA.1 and BA.2...