Omicron could come from animals
The origin of the many mutations in the spike protein in this scenario would be the pressure to adapt as well as possible to the new animal host and its ACE2 receptors. That would also go together with the rather strong selection pressure on the spike protein. In addition, the characteristic changes in the omicron variant could possibly contain traces of animal origin. Experts have been looking for such clues since the beginning of the pandemic: They also collect sequences that they find in animals infected with Sars-CoV-2 – be it tigers in a zoo or mice in the laboratory.
Because of this, there is a whole catalog of mutations in the spike protein and in the animals in whose viruses the changes have appeared. And there is one thing that is noticeable. So the Immunologist Kristian G. Andersen, who considers an animal origin for Omikron to be the most plausible, make sure that you have several knows the mutations in the antigen-binding domain of the spike protein, which are typical for Omikron, also from virus lines in mice.
Another argument in favor of animal origin is the fact that Omikron contains some new and unique mutations. In addition, Sars-CoV-2 infects many animals and that the virus can jump to animals and back to humans has already been observed in minks. On the other hand, large parts of the mutations of Omikron can be explained just as well or even better with an evolution in humans. In addition, the variety of Sars-CoV-2 in humans is so extremely much greater that it appears statistically unlikely that a globally significant variant like Omikron will emerge from such a narrow niche, of all places. But that too is speculation: So far there is no data on the interactions between a pandemic and animal reservoirs.
This also applies to the open questions that arise with the other two hypotheses. While there are various case reports and genetic sequences from long-term infected people with immunosuppression, no one knows how well such mutated viruses really do. It is not even certain that one of the three options is correct – Omikron may be the product of completely different circumstances. Even people with a healthy immune system could, in rare cases, be infected for a long time and breed strongly modified variants. So what actually happened in the 15 months or so between the last known forerunner of Omikron and the appearance of the very strongly mutated new variant is currently unknown.