Isn't it kind of insane that BA.1 might have infected billions worldwide but BA.2, which emerged from the same host/reservoir a month later or so, is looking like to outcompete all of these BA.1 lineages?
It's also noteworthy that BA.2 is likely a recombinant virus, sharing every mutation past the NTD portion of the spike with BA.1 but being a thing of its own before that spot. It turns out this is a template-switching location and some delta/omicron recombinants from January also split around the same spot.
So the evolutionary history of Omicron is looking like:
1. B.1.1 virus gets in an animal reservoir/immunosupressed person in early 2020, evolves throughout the next 18 months;
2. Said person or reservoir also gets infected with a 'pristine' SARS-CoV-2 mystery lineage;
3. "Ancestral Omicron" (already sharing almost all BA.1 mutations) recombines with mystery lineage at the beginning (BA.3) or middle of the NTD portion of the spike (BA.2) before mystery lineage vanishes;
4. BA.1 emerges from "ancestral Omicron", BA.2 and BA.3 emerge at a later date.
