An immediate hypothesis was that Omicron may have developed in a single immunocompromised human patient over a period of weeks or months[: … y]ou don’t just immediately kill everything off - you give the virus or bacterium a chance to overcome a lesser challenge before turning up the pressure a bit more, letting mutations accumulate and try their worth over and over as the challenge slowly increases. That’s just what’s going on inside a coronavirus patient if they can’t mount a full immune response. The virus and the immune system engage in a prolonged battle where neither one can land a decisive blow, and things just keep on evolving. This is why they tell you to take your full course of antibiotics when you have a bacterial infection, and why effective vaccines actually suppress variant formation: if you kill off the pathogens as quickly as possible, they don’t have time to explore their mutational landscape
Prolonged battles are not one by either party that started them. The participant is usually changed along the way such that the winner is neither that started.
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