Recombination can explain #2 pretty easily. Chronic infection produced many mutations, it also did that across many HIV infected individuals in South Africa.

Recombination can explain #2 pretty easily. Chronic infection produced many mutations, it also did that across many HIV infected individuals in South Africa. Those infections mutated via natural selection to avoid in-host immune responses and actually transmit poorly in the population. One of these chronically infected individuals recently came into contact with someone else that was recently infected with circulating virus. The doubly infected individual allowed Omicron to mutate via recombination and pick up mutations that allow it to spread better and so it took off. This is also more or less how animal spillback would happen as well. The animal type should be better animal-adapted and not better human-adapted. You probably need a recombination event to spill it back effectively.