Omicron appeared out the blue less than a month ago in S. Africa and is spreading very quickly. Rachel Walensky of the CDC, said today (14 December 2021) that it currently accounts for 13% of cases in New York and New Jersey.
Where did it come from? An analogy might help the nonvirologist. Lots of things evolve, even musical instruments. The Museum of Fine Arts in Boston has a room with old instruments, some of which are decidedly weird and vanished without a trace. Others show an obvious evolution, particularly keyboard, string and wind instruments. A cellist can see how it evolved from the gamba, and a keyboard player can see how the piano came from the harpsichord. Omicron is so different from its predecessors that it’s like a tuba coming from a clavichord with no intermediate steps.
This is exactly the way scientists saw it initially [ Science vol. 374 pp. 1178 – 1180 3 December ’21 ] https://www.science.org/doi/epdf/10.1126/science.acx9737
The first diagram shows it best, with a plot of the number of mutations from the original sequence in early 2020. Gradually the number of mutations in successful viruses crept up one by one to about 15. Enter omicron which suddenly has 30 (15 of them new).
Three possible scenarios for its appearance are given
l. The virus was evolving in a population with no surveillance
2. The virus came from an infected patient who was immunodeficient, who fought the virus to a draw allowing it to mutate for months — there is a well documented precedent for this sort of thing happening [ Nature vol. 592 pp. 277 – 282 ’21 ]
3. It might have evolved in animals, only recently spilling over to man (a la AIDS)
It was early times and the excellent author Kai Kupferschmidt whose article this is and whose articles are always worth reading, couldn’t have known about what was to appear in the 9 December Nature [ vol. 600 p. 197 – 199 ’21 ]. https://media.nature.com/original/magazine-assets/d41586-021-03614-z/d41586-021-03614-z.pdf.
A virologist engineered a viral protein with mutations which was able to evade antibodies produced by the 3 extant vaccines used in the USA. You can read about it here — https://www.rockefeller.edu/news/31153-could-future-coronavirus-variants-fully-dodge-our-immune-system/. They selected for the mutations in the spike protein which were resistant, and then put TWENTY of them in the spike protein.
Here is a direct quote from the article — ”
For the study, they first created a safe stand-in for the coronavirus by tweaking a different, harmless virus to express SARS-CoV-2 spike protein on its surface. As the faux coronaviruses replicated, some picked up mutations as they made mistakes copying themselves. The team then bathed the faux coronaviruses in plasma samples from people who had recovered from COVID, and selected the mutants that escaped neutralization by antibodies. A few rounds of this and the team found many mutations that were in the same locations as those occurring naturally in SARS-CoV-2 variants, including those found in Delta or other variants of concern.
The researchers then created a “polymutant” virus: a faux coronavirus sporting a spike protein featuring 20 of the worst of those mutations all at once. This polymutant showed near-complete resistance to antibodies generated by individuals who have been infected by or vaccinated against SARS-CoV-2.”
This is a far more likely (and frightening) story for the origin of omicron. The technology is available and widespread. The virus is so different with no intermediate viruses known that a lab origin is more likely than the 3 explanations given above. It makes more sense to me and I hope I’m wrong; but if I’m not there will be others: and some of them could well be used as bioweapons. It is even possible that omicron is the first (or the second depending on how paranoid you are).
Chemiotics II 
Comments
It might had evolved in the immunocompromised individual with persistent infection
Agree, this was noted in one of the articles cited and in the post
2. The virus came from an infected patient who was immunodeficient, who fought the virus to a draw allowing it to mutate for months — there is a well documented precedent for this sort of thing happening [ Nature vol. 592 pp. 277 – 282 ’21 ]